diff --git a/224TMHexane/Gromacs/T293highP_Viscosity/Potoff_N200_LINCS/README b/224TMHexane/Gromacs/T293highP_Viscosity/Potoff_N200_LINCS/README
new file mode 100644
index 0000000..ae80d0d
--- /dev/null
+++ b/224TMHexane/Gromacs/T293highP_Viscosity/Potoff_N200_LINCS/README
@@ -0,0 +1 @@
+This is the folder where Mohammad's output should go
\ No newline at end of file
diff --git a/Scripts/AlkanesViscosity.sh b/Scripts/AlkanesViscosity.sh
index 073b254..bdd3b90 100644
--- a/Scripts/AlkanesViscosity.sh
+++ b/Scripts/AlkanesViscosity.sh
@@ -1,933 +1,933 @@
-#!/bin/bash
-source /usr/local/gromacs/bin/GMXRC
-####
-#
-#This code submits a set of CH3 and CH2 parameter sets (determined by Bayesian MCMC with a different code)
-#Simulations are performed at 5 conditions read from files.
-#Temperatures are performed sequentially, batches of NREPS parameter sets are submitted at a time
-#Green-Kubo analysis is used after each temperature loop is completed
-#
-#
-####
-
-### IN ORDER TO CALCULATE RDF FUNCTIONS:
-# The groups specified by refs and sels (see below)
-# must be specified in the original compound's .gro file
-# Check that the names given in the .gro file are the names
-# which actually appear in the index file if there are problems.
-# Trajectory files must exists for the NVT production run
-###
-
-### IN ORDER TO RUN NEMD
-# 
-###
-
-# Gives a more informative error when something goes wrong
-# with the script.
-error_report() {
-echo "Error $1 on j $2, iMCMC $3, stage $4"
-exit 1
-}
-
-clean() {   # Make it so everything is killed on an interrupt
-local pids=$(jobs -pr)
-echo "On exit sending kill signal to: $pids"
-[ -n "$pids" ] && kill $pids
-exit 1
-}
-trap "clean" SIGINT SIGTERM EXIT SIGQUIT  # Call cleanup when asked to
-
-job_date=$(date "+%Y_%m_%d_%H_%M_%S")
-
-Compound=224TMHexane
-Model=Potoff
-Conditions_type=T293highP    #Saturation         #"$Model"_Saturation   #Saturation # ie T293highP
-BondType=LINCS  #Harmonic (flexible) or LINCS (fixed)
-Temp=293  # Default temp, used if no temperature file is found in conditions path
-jlim=13  # Upper bound on j; condition sets to run; exclusive. Should usually be 5
-jlow=12  # Lower bound on j; inclusive. needed in special cases. Should usually be 0
-batches=1  # Number of batches to run
-NREPS=1 #Run NREPS replicates in parallel/# in a batch (Overriden by NEMD=YES)
-pin0=0  # Default pinoffset, used to tell taskset where to run jobs
-nt_eq=1  # Thread number during equilibration
-nt_vis=1  # This thread number will serve in production and viscosity runs
-NPT=YES # YES indicates NPT runs should be carried out prior to NVT runs (YES or NO)
-#echo "CHANGE THIS BACK BEFORE RUNNING MORE T293highP!!!"
-NEMD=NO  # Calculate viscosity using the periodic perturbation method  (YES or NO)
-RDF=NO  # Whether to perform RDF calculations (YES or NO)
-MCMC_tors=NO # YES indicates model includes torsional uncertainties
-#Set the number of molecules
-Nmol=200
-
-
-###### STEP SIZE INFORMATION #######
-# Runtiming control: override default runtimes=YES, otherwise use NO
-OVERRIDE_STEPS=YES
-# If OVERRIDE_STEPS=YES, arrays must be of length j 
-# indicating how many equilibration and production steps,
-# respectively, to perform for each j
-#equil_steps=(500000 500000 500000 500000 500000)
-#prod_steps=(500000 500000 500000 500000 500000)
-equil_steps=(500000 500000 500000 500000 500000 500000 500000 500000 500000 500000 500000 500000 500000)
-prod_steps=(500000 500000 500000 500000 500000 1000000 2000000 4000000 4000000 8000000 8000000 12000000 24000000)
-
-# The mdp path is decided later based on the kind of run, but in the case that Lennard Jones
-# mdp's will be used, the lj_mdp_path will be the variable selected, otherwise t_mdp_path will be used.
-lj_mdp_path=~/LennardJones
-t_mdp_path=~/Tabulated
-
-#### RDF INFORMATION #####
-RDF_single=NO   # Only perform one RDF run for each j (YES or NO)
-rdfs=2  # Number of RDF functions to produce for each NVT production run
-refs=(H2 H3)  # The references for RDF computation; length must equal rdfs
-sels=(H2 H3)  # The other group in the RDF computation
-cut_rdf=.2  # Cutoff for interactions calculated by RDF
-
-#### NEMD INFORMATION #######
-if [ "$NEMD" = "YES" ]
-then
-NEMD_pts=10  # Number of different cos-accelerations to use
-cos_acc=(.01 .02 .03 .04 .05 .06 .07 .08 .09 .1)
-NREPS=$NEMD_pts
-fi
-
-#Specify the path location for files
-scripts_path=~/Scripts
-conditions_path=~/"$Conditions_type"_Conditions  
-exp_data_path=~/TDE_REFPROP_values
-input_path=~/"$Compound"/Gromacs/Gromacs_input
-if [ "$NEMD" = "YES" ]
-then
-output_path=~/"$Compound"/Gromacs/"$Conditions_type"_Viscosity/"$Model"_N"$Nmol"_"$BondType"_NEMD #Code assumes that a folder already exists with this directory and the eps_sig_lam_MCMC file in it
-else
-output_path=~/"$Compound"/Gromacs/"$Conditions_type"_Viscosity/"$Model"_N"$Nmol"_"$BondType" 
-fi
-
-if [ "$MCMC_tors" = "YES" ]
-then
-output_path="$output_path"_MCMC_tors
-echo "Using MCMC derived torsional parameters"
-
-else
-
-echo "Using fixed literature values for torsional parameters"
-
-fi
-
-jobfile="$output_path"/"$Compound"_job_"$job_date" 
-cp "$scripts_path"/AlkanesViscosity.sh "$jobfile" #Keep track of what jobs have been submitted
-cat "$scripts_path"/nAlkanesNPTsteps >> "$jobfile"  # Inellegant append
-cat "$scripts_path"/run_single.sh >> "$jobfile"  # Another inellegant append
-touch "$output_path"/warnings_job_"$job_date"
-
-cd "$output_path" || error_report "Error switching to $output_path" "0" "0" "preprocessing"
-
-touch press_all_log
-touch Lbox_all
-
-### Read the box size, that depends on number of molecules
-if [ -f "$conditions_path"/"$Compound"_liquid_box_N"$Nmol" ]
-then
-
-while read line
-do 
-liquid_box+=("$line")
-done < "$conditions_path"/"$Compound"_liquid_box_N"$Nmol"
-
-else
-echo "Unable to read box from $conditions_path"/"$Compound"_liquid_box_N"$Nmol"
-exit 1
-fi
-
-# If pressure data is needed for an NPT run,
-# Determine whether or not the pressure data is available.
-if [ "$NPT" = "YES" ]
-then
-if [ -f "$conditions_path"/"$Compound"_press ]
-then
-echo Pressures ${press[@]} read from "$conditions_path"/"$Compound"_press
-else
-echo Pressures could not be read from "$conditions_path"/"$Compound"_press
-exit 1
-fi
-
-### Read the pressure file into the array 'press'
-while read line
-do
-press+=("$line")
-done < "$conditions_path"/"$Compound"_press
-fi
-
-### Determine Temperature. In some cases temperature should be read from a file
-# IF a temperature file exists, it will use that 
-temp_search_path="$conditions_path"/"$Compound"_Temp
-if [ "$Conditions_type" = "Saturation" ] || [ "$Conditions_type" = "$Model"_"Saturation" ]
-then
-temp_search_path="$conditions_path"/"$Compound"_Tsat
-fi
-echo Looking for temperatures at "$temp_search_path"
-if [ -e "$temp_search_path" ]
-then
-while read line
-do 
-temps+=("$line")
-done < "$temp_search_path"
-
-# Otherwise, fill the array with copies of the given temperature
-# Make the array the same length as the pressure
-echo Temperatures ${temps[@]} read from "$temp_search_path"
-else
-for ((x=0; x < ${#liquid_box[@]}; x++))  # C style loop 
-do
-temps+=("$Temp")
-done
-echo Temperatures ${temps[@]} from default temperature used
-fi
-
-###Equilibration time is different for certain compounds
-# 0.002 ps time step
-
-if [ "$Compound" = 'C3H8' ]
-then
-
-nsteps_eq=50000 # 0.1 ns total
-
-elif [ "$Compound" = 'C4H10' ]
-then
-
-nsteps_eq=100000 # 0.2 ns total
-
-else
-
-nsteps_eq=500000 # 1 ns total
-
-fi
-
-# We're going to ignore normal step sizes
-if [ "$OVERRIDE_STEPS" = "YES" ]
-then
-echo Overriding step numbers using equil=${equil_steps[*]}, prod=${prod_steps[*]}
-# Use predefined step sizes
-else
-for ((x=0; x < jlim; x++))
-do
-equil_steps[$x]=$nsteps_eq
-prod_steps[$x]=500000
-done
-fi
-echo Step numbers : equil=${equil_steps[*]}, prod=${prod_steps[*]}
-
-
-###Cut-off distance is different for some force fields
-if [ "$Model" = 'Potoff' ]
-then
-
-rvdw=1.0 # [nm]
-
-else
-
-rvdw=1.4 # [nm]
-
-fi
-
-### Assign force field parameters
-if [ "$Model" = 'TraPPE' ]
-then
-
-#TraPPE
-
-bondlength_CH3=0.1540
-
-epsCH3_sim=98. # (K)
-sigCH3_sim=0.375 # (nm)
-lamCH3_sim=12.0
-
-epsCH2_sim=46. # (K)
-sigCH2_sim=0.395 # (nm)
-lamCH2_sim=12.0
-
-epsCH_sim=10. # (K)
-sigCH_sim=0.468 # (nm)
-lamCH_sim=12.0
-
-epsC_sim=0.5 # (K)
-sigC_sim=0.640 # (nm)
-lamC_sim=12.0
-
-lam_sim=12.0
-
-elif [ "$Model" = 'TraPPEAUA' ]
-then
-
-#TraPPE_AUA
-
-bondlength_CH3=0.192
-
-epsCH3_sim=134.5 # (K)
-sigCH3_sim=0.352 # (nm)
-lamCH3_sim=12.0
-
-#Borrow the rest from TraPPE-UA
-
-epsCH2_sim=46. # (K)
-sigCH2_sim=0.395 # (nm)
-lamCH2_sim=12.0
-
-epsCH_sim=10. # (K)
-sigCH_sim=0.468 # (nm)
-lamCH_sim=12.0
-
-epsC_sim=0.5 # (K)
-sigC_sim=0.640 # (nm)
-lamC_sim=12.0
-
-lam_sim=12.0
-
-elif [ "$Model" = 'Potoff' ]
-then
-
-#Potoff
-
-bondlength_CH3=0.1540
-
-epsCH3_sim=121.25 # (K)
-sigCH3_sim=0.3783 # (nm)
-lamCH3_sim=16.0
-
-epsCH2_sim=61. # (K)
-sigCH2_sim=0.399 # (nm)
-lamCH2_sim=16.0
-
-#S/L
-if [ "$Compound" = 'IC4H10' ] || [ "$Compound" = 'IC5H12' ] || [ "$Compound" = 'NEOC5H12' ] || [ "$Compound" = '23DMButane' ]
-then
-
-#Short (4 or fewer C backbone)
-epsCH_sim=15.00 # (K)
-sigCH_sim=0.470 # (nm)
-lamCH_sim=16.0
-
-epsC_sim=1.45 # (K)
-sigC_sim=0.610 # (nm)
-lamC_sim=16.0
-
-echo "You are using short CH and C parameters"
-
-elif [ "$Compound" = 'IC6H14' ] || [ "$Compound" = 'IC8H18' ] || [ "$Compound" = '3MPentane' ] || [ "$Compound" = '224TMHexane' ]
-then
-
-#Long (5 or more C backbone)
-epsCH_sim=14.00 # (K)
-sigCH_sim=0.470 # (nm)
-lamCH_sim=16.0
-
-epsC_sim=1.2 # (K)
-sigC_sim=0.620 # (nm)
-lamC_sim=16.0
-
-echo "You are using long CH and C parameters"
-
-else
-
-# Transferable sites
-epsCH_sim=15.00 # (K)
-sigCH_sim=0.460 # (nm)
-lamCH_sim=16.0
-
-epsC_sim=0.5 # (K)
-sigC_sim=0.610 # (nm)
-lamC_sim=16.0
-
-echo "You are using transferable CH and C parameters"
-
-fi
-
-lam_sim=16.0
-
-elif [ "$Model" = 'TAMie' ]
-then
-
-#TAMie
-
-bondlength_CH3=0.174
-
-epsCH3_sim=136.318 # (K)
-sigCH3_sim=0.36034 # (nm)
-lamCH3_sim=14.0
-
-epsCH2_sim=52.9133 # (K)
-sigCH2_sim=0.404 # (nm)
-lamCH2_sim=14.0
-
-epsCH_sim=14.5392 # (K)
-sigCH_sim=0.43656 # (nm)
-lamCH_sim=14.0
-
-epsC_sim=0.0 # (K)
-sigC_sim=0.0 # (nm)
-lamC_sim=14.0
-
-lam_sim=14.0
-
-elif [ "$Model" = 'AUA4' ]
-then
-
-#AUA4
-
-if [ "$Compound" = 'C2H6' ]
-then
-
-bondlength_CH3=0.196668
-
-else
-
-bondlength_CH3=0.1751
-
-fi
-
-epsCH3_sim=120.15 # (K)
-sigCH3_sim=0.36072 # (nm)
-lamCH3_sim=12.0
-
-epsCH2_sim=86.29 # (K)
-sigCH2_sim=0.3431 # (nm)
-lamCH2_sim=12.0
-
-epsCH_sim=50.98 # (K)
-sigCH_sim=0.3363 # (nm)
-lamCH_sim=12.0
-
-epsC_sim=15.04 # (K)
-sigC_sim=0.244 # (nm)
-lamC_sim=12.0
-
-lam_sim=12.0
-
-#Standard CC bondlength for AUA4 = 0.1535 nm
-#delta_CH3=0.0216 nm
-#delta_CH2=0.0384 nm
-#delta_CH=0.0646 nm
-
-else
-
-bondlength_CH3=0.154 #(nm)
-
-fi
-
-if [ "$lam_sim" = 12.0 ]
-then
-
-echo "Using native Lennard-Jones potential"
-mdp_path="$lj_mdp_path"
-#Originally I tried to have a tab_flag variable, but it was not working for tabulated because
-#using "$tab_flag" in mdrun was different than echo. Fortunately, I discovered that Gromacs
-#will just ignore the provided table if the vdwtype is cut-off instead of user.
-#tab_flag=""
-
-else
-
-echo "Using tabulated potential"
-mdp_path="$t_mdp_path"
-#This also required copying tab_it into the output_path whereas it is typically output_path/MCMC_iMCMC
-#tab_flag="-table $output_path/tab_it.xvg "
-
-fi
-
-### Copy experimental data files to output directory
-
-# Copy in appropriate data for later post processing
-if [ "$Conditions_type" = "Saturation" ]
-then
-cp "$exp_data_path"/"$Compound"_TDE_eta_sat.txt "$output_path"/TDE_eta_sat.txt
-cp "$exp_data_path"/"$Compound"_REFPROP_eta_sat.txt "$output_path"/REFPROP_eta_sat.txt
-else
-cp "$exp_data_path"/"$Compound"_REFPROP_eta_"$Conditions_type".txt "$output_path"/REFPROP_eta_"$Conditions_type".txt
-fi
-
-
-### Create file and header for state point conditions if not already created
-if [ ! -e "$output_path"/"$Conditions_type"Settings.txt ]
-then
-echo "NMol" "Length (nm)" "Temp (K)" > "$output_path"/"$Conditions_type"Settings.txt	
-fi
-
-### Loop through temperatures and densities		
-jlim=$((jlim - 1))
-batches=$((batches - 1))  # Limits for 0 indexed loops later
-
-for j in $(seq $jlow $jlim) # Number of conditions to run
-
-do
-
-### Record state points
-echo "$Nmol" "${liquid_box[j]}" "${temps[j]}" >> "$output_path"/"$Conditions_type"Settings.txt
-
-nRep=0
-
-NREP_low=0
-NREP_high=$((NREPS-1))
-
-#NREP_low=$((NREP_low+20+15))
-#NREP_high=$((NREP_high+20+15))
-
-####
-
-for iRep in $(seq 0 $batches) # Number of batches to run (0 9), 10 batches with 20 replicates is 200 parameter sets
-
-do
-
-for iMCMC in $(seq $NREP_low $NREP_high)
-do
-
-cd "$output_path" || error_report "Unable to change to $output_path" "$j" "$iMCMC" "start up" 
-
-### Read in eps, sig, and lam from a file that contains the MCMC samples
-
-if [ "$Model" = 'MCMC_lam16' ]
-then
-
-epsCH3_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print $1}' < ~/MCMC_parameter_sets/eps_sig_lam16_MCMC_CH3_CH2_CH_C)
-sigCH3_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print $2}' < ~/MCMC_parameter_sets/eps_sig_lam16_MCMC_CH3_CH2_CH_C)
-lam_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print $3}' < ~/MCMC_parameter_sets/eps_sig_lam16_MCMC_CH3_CH2_CH_C)
-epsCH2_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print $4}' < ~/MCMC_parameter_sets/eps_sig_lam16_MCMC_CH3_CH2_CH_C)
-sigCH2_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print $5}' < ~/MCMC_parameter_sets/eps_sig_lam16_MCMC_CH3_CH2_CH_C)
-epsCH_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print $7}' < ~/MCMC_parameter_sets/eps_sig_lam16_MCMC_CH3_CH2_CH_C)
-sigCH_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print $8}' < ~/MCMC_parameter_sets/eps_sig_lam16_MCMC_CH3_CH2_CH_C)
-epsC_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print $10}' < ~/MCMC_parameter_sets/eps_sig_lam16_MCMC_CH3_CH2_CH_C)
-sigC_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print $11}' < ~/MCMC_parameter_sets/eps_sig_lam16_MCMC_CH3_CH2_CH_C)
-
-fi
-
-#if [ "$MCMC_tors" = "YES" ]
-#then
-#
-#CH2_CH2_tors_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print $1}' < ~/MCMC_parameter_sets/MCMC_CH2_CH2_tors)
-#CH2_CH_tors_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print $2}' < ~/MCMC_parameter_sets/MCMC_CH2_CH_tors)
-#CH2_C_tors_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print $3}' < ~/MCMC_parameter_sets/MCMC_CH2_C_tors)
-#CH_CH_tors_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print $4}' < ~/MCMC_parameter_sets/MCMC_CH_CH_tors)
-#
-#fi
-
-echo iMCMC = "$iMCMC"
-
-echo Run "$Conditions_type" Viscosity for epsCH3 = "$epsCH3_sim" sigCH3 = "$sigCH3_sim" lamCH3 = "$lam_sim" epsCH2 = "$epsCH2_sim" sigCH2 = "$sigCH2_sim" lamCH2 = "$lam_sim" epsCH = "$epsCH_sim" sigCH = "$sigCH_sim" lamCH = "$lam_sim" epsC = "$epsC_sim" sigC = "$sigC_sim" lamC = "$lam_sim"
-
-####
-
-mkdir -p MCMC_"$iMCMC"
-cd MCMC_"$iMCMC" || error_report "Unable to change to MCMC_$iMCMC" "$j" "$iMCMC" "start up"
-
-###Create files with force field parameters
-bash "$scripts_path"/force_field_params "$Compound" "$input_path" "$scripts_path" "$lam_sim" "$epsCH3_sim" "$sigCH3_sim" "$epsCH2_sim" "$sigCH2_sim" "$epsCH_sim" "$sigCH_sim" "$epsC_sim" "$sigC_sim" "$bondlength_CH3" "$Nmol" "$MCMC_tors" "$iMCMC"  #"${CH2_CH2_tors_sim[@]}" "${CH2_CH_tors_sim[@]}" "${CH2_C_tors_sim[@]}" "${CH_CH_tors_sim[@]}"
-
-### Copy tab_it.xvg to previous directory, assumes that all MCMC parameter sets use the same value of lambda
-#Not needed anymore
-#cp tab_it.xvg ../tab_it.xvg
-
-### Record state points, include header if creating file
-### Moved this outside of loop
-#if [ -e "$output_path"/MCMC_"$iMCMC"/"$Conditions_type"Settings.txt ]
-#then
-#echo "NMol" "Length (nm)" "Temp (K)" > "$output_path"/MCMC_"$iMCMC"/"$Conditions_type"Settings.txt
-#fi
-
-# Initialize the folders, copy files, and insert variables
-
-cd "$output_path"/MCMC_"$iMCMC" || error_report "Unable to change to directory MCMC_$iMCMC" "$j" "$iMCMC" "start up"  #presumes this dir was made previously
-
-mkdir -p Saturated
-cd Saturated || error_report "Unable to change to directory Saturated" "$j" "$iMCMC" "start up" 
-
-mkdir -p rho"$j"
-cd    rho"$j" || error_report "Unable to change to directory rho$j" "$j" "$iMCMC" "start up"
-
-#echo "$Nmol" "${liquid_box[j]}" "${Temp}" >> "$output_path"/MCMC_"$iMCMC"/"$Conditions_type"Settings.txt
-
-mkdir -p Rep"$nRep"  
-cd    Rep"$nRep" || error_report "Unable to change to directory Rep$nRep" "$j" "$iMCMC" "start up"
-
-gmx insert-molecules -ci ../../../"$Compound".gro -nmol "$Nmol" -try 2000 -box "${liquid_box[j]}" "${liquid_box[j]}" "${liquid_box[j]}" -o "$Compound"_box.gro > insertout 2>> insertout
-
-if [ "$RDF" = "YES" ]  # Do RDF setup
-then
-rdf_lim=$((rdfs - 1))  # Will be needed later for RDF computational loop
-# Create the index file for later- pipes the necessary quit command to the interactive tool
-echo q | gmx make_ndx -f "$Compound"_box.gro -o index.ndx > make_ndx.out 2>> make_ndx.out  
-fi
-
-#Copy the minimization files
-echo mdp_path "$mdp_path"
-cp "$mdp_path"/em_steep.mdp em_steep.mdp
-cp "$mdp_path"/em_l-bfgs.mdp em_l-bfgs.mdp
-
-sed -i -e s/some_rvdw/"$rvdw"/ em_steep.mdp
-sed -i -e s/some_rvdw/"$rvdw"/ em_l-bfgs.mdp
-
-mkdir -p NVT_eq
-cd NVT_eq || error_report "Unable to change to directory NVT_eq" "$j" "$iMCMC" "start up"
-
-# Copy the equilibration files and edit the temperature
-
-cp "$mdp_path"/nvt_eq_no_output_"$BondType".mdp nvt_eq.mdp
-sed -i -e s/some_temperature/"${temps[j]}"/ nvt_eq.mdp
-sed -i -e s/some_nsteps/"${equil_steps[j]}"/ nvt_eq.mdp
-sed -i -e s/some_rvdw/"$rvdw"/ nvt_eq.mdp
-cur_ind=$((iMCMC - NREP_low))  # Find the proper cos_acceleration and subsitute
-sed -i -e s/some_cos_acceleration/"${cos_acc[cur_ind]}"/ nvt_eq.mdp
-
-# Still creating NVT_prod directory so that our codes are backwards compatible with data analysis (i.e. same directory hierarchy)
-
-mkdir -p NVT_prod
-cd NVT_prod || error_report "Unable to change to directory NVT_prod" "$j" "$iMCMC" "start up"
-# Create new directory for viscosity run
-
-mkdir -p NVT_vis
-cd NVT_vis || error_report "Unable to change to directory NVT_vis" "$j" "$iMCMC" "start up"
-
-# Copy the viscosity files and edit the temperature
-
-cp "$mdp_path"/nvt_vis_no_xv_"$BondType".mdp nvt_vis.mdp
-sed -i -e s/some_temperature/"${temps[j]}"/ nvt_vis.mdp
-sed -i -e s/some_nsteps/"${prod_steps[j]}"/ nvt_vis.mdp
-sed -i -e s/some_rvdw/"$rvdw"/ nvt_vis.mdp
-sed -i -e s/some_cos_acceleration/"${cos_acc[cur_ind]}"/ nvt_vis.mdp
-
-done # for loop over iMCMC
-
-### Run the NPT steps to determine the box sizes
-# Skip this if NPT != YES
-if [ "$NPT" = "YES" ]
-then
-bash "$scripts_path"/nAlkanesNPTsteps "$Compound" "$Nmol" "${liquid_box[j]}" "$mdp_path" "$BondType" "${temps[j]}" "${press[j]}" "${equil_steps[j]}" "$rvdw" "$NREP_low" "$NREP_high" "$output_path" "$j" "$nRep" "$scripts_path" "$pin0" "$nt_eq" "$nt_vis" "${prod_steps[j]}"
-fi
-
-###First energy minimization
-
-pinoffset=$pin0
-
-for iMCMC in $(seq $NREP_low $NREP_high)
-do
-
-echo pinoffset = "$pinoffset"
-
-cd "$output_path"/MCMC_"$iMCMC"/Saturated/rho"$j"/Rep"$nRep" || exit  #start fresh for do cycle instead of multiple "cd .."'s
-
-gmx grompp -f em_steep.mdp -c "$Compound"_box.gro -p ../../../"$Compound".top -o em_steep.tpr > gromppout 2>> gromppout
-#We now use a different approach for assigning nodes
-#gmx mdrun -table "$output_path"/MCMC_"$iMCMC"/tab_it.xvg -pin on -pinoffset "$pinoffset" -pinstride 1 -ntomp 1 -nt 1 -nb cpu -deffnm em_steep > runout 2>> runout &
-gmx mdrun -table "$output_path"/MCMC_"$iMCMC"/tab_it.xvg -nt 1 -nb cpu -pme cpu -deffnm em_steep > runout 2>> runout &
-#gmx mdrun -table "$output_path"/MCMC_"$iMCMC"/tab_it.xvg -nt 1 -nb cpu -deffnm em_steep > runout 2>> runout &
-cur_pid=$!
-taskset -cp "$pinoffset" $cur_pid > /dev/null 2>&1
-min_3_pids[${iMCMC}]=$cur_pid  # This is the third such step (others are in the subscript) hence 3
-
-pinoffset=$((pinoffset+1))
-
-done #for iMCMC
-
-echo "Waiting for em_steep.tpr: Energy Minimization Part1"
-
-for pid in ${min_3_pids[*]}  # Loop over array
-do 
-wait $pid
-done
-
-###Second energy minimization
-
-pinoffset=$pin0
-
-for iMCMC in $(seq $NREP_low $NREP_high)
-do
-
-echo pinoffset = "$pinoffset"
-
-cd "$output_path"/MCMC_"$iMCMC"/Saturated/rho"$j"/Rep"$nRep" || error_report "Unable to change to directory Rep$nRep" "$j" "$iMCMC" "second energy minimzation NVT"  #start fresh for do cycle instead of multiple "cd .."'s
-
-gmx grompp -f em_l-bfgs.mdp -c em_steep.gro -p ../../../"$Compound".top -o em_l_bfgs.tpr -maxwarn 1 >> gromppout 2>> gromppout
-#gmx mdrun -table "$output_path"/MCMC_"$iMCMC"/tab_it.xvg -pin on -pinoffset "$pinoffset" -pinstride 1 -ntomp 1 -nt 1 -nb cpu -deffnm em_l_bfgs >> runout2 2>> runout2 &
-gmx mdrun -table "$output_path"/MCMC_"$iMCMC"/tab_it.xvg -nt 1 -nb cpu -pme cpu -deffnm em_l_bfgs > runout2 2>> runout2 &
-#gmx mdrun -table "$output_path"/MCMC_"$iMCMC"/tab_it.xvg -nt 1 -nb cpu -deffnm em_l_bfgs > runout2 2>> runout2 &
-cur_pid=$!
-taskset -cp "$pinoffset" $cur_pid > /dev/null 2>&1
-min_4_pids[${iMCMC}]=$cur_pid
-
-pinoffset=$((pinoffset+1))
-
-done #for iMCMC
-
-echo "Waiting for second energy minimization"
-
-for pid in ${min_4_pids[*]}  # Iterate over 4th minimization array
-do
-wait $pid
-done
-
-###Equilibration period
-
-pinoffset=$pin0
-
-for iMCMC in $(seq $NREP_low $NREP_high)
-do
-
-echo pinoffset = "$pinoffset"
-
-cd "$output_path"/MCMC_"$iMCMC"/Saturated/rho"$j"/Rep"$nRep"/NVT_eq || error_report "Unable to change to NVT_eq directory" "$j" "$iMCMC" "NVT equilibrium"  #start fresh for do cycle instead of multiple "cd .."'s
-
-if ls ../step*.pdb 1> /dev/null 2>&1 #Remove these warning files
-then
-echo some energy minimizations might have failed for "$output_path"/MCMC_"$iMCMC"/Saturated/rho"$j"/Rep"$nRep" >> "$output_path"/warnings_job_"$job_date"
-rm ../step*.pdb
-fi
-
-gmx grompp -f nvt_eq.mdp -c ../em_l_bfgs.gro -p ../../../../"$Compound".top -o nvt_eq.tpr > gromppout 2>> gromppout
-#gmx mdrun -table "$output_path"/MCMC_"$iMCMC"/tab_it.xvg -pin on -pinoffset "$pinoffset" -pinstride 1 -nt "$nt_eq" -nb cpu -deffnm nvt_eq > runout 2>> runout &
-Tempbox=${liquid_box[j]}  # This is the default for no NPT
-if [ $NPT = YES ]
-then
-Tempbox=$(<../NPT_eq/NPT_prod/Lbox_NPT_ave)  # This is the default for NPT
-fi
-# Pass the proper box size to the subscript in case it needs to restart calculations (it starts from insert molecules)
-bash "$scripts_path"/run_single.sh "$output_path"/MCMC_"$iMCMC"/tab_it.xvg "$nt_eq" cpu cpu nvt_eq "$pinoffset" "$j" "$nRep" "$output_path" "$NREP_low" "$NREP_high" "$Compound" "$Nmol" "$Tempbox" nvt &
-
-pinoffset=$((pinoffset+nt_eq))
-
-done #for iMCMC
-
-echo Waiting for "$Conditions_type" equilibration
-
-nit=0
-maxit=3000000
-ndone=$(cat "$output_path"/MCMC_*/Saturated/rho"$j"/Rep"$nRep"/NVT_eq/runout | grep -c "GROMACS reminds you")
-while [ $ndone -lt $((NREP_high+1)) ] && [ $nit -lt $maxit ]
-do
-nit=$((nit+1))
-sleep 100s 
-echo Waiting for "$Conditions_type" equilibration
-ndone=$(cat "$output_path"/MCMC_*/Saturated/rho"$j"/Rep"$nRep"/NVT_eq/runout | grep -c "GROMACS reminds you")
-done
-
-###Removed production period
-
-###Viscosity period
-
-pinoffset=$pin0
-for iMCMC in $(seq $NREP_low $NREP_high)
-do
-
-echo pinoffset = "$pinoffset"
-
-cd "$output_path"/MCMC_"$iMCMC"/Saturated/rho"$j"/Rep"$nRep"/NVT_eq/NVT_prod/NVT_vis || error_report "Unable to change to directory NVT_vis" "$j" "$iMCMC" "NVT viscosity"  #start fresh for do cycle instead of multiple "cd .."'s
-
-gmx grompp -f nvt_vis.mdp -c ../../nvt_eq.gro -p ../../../../../../"$Compound".top -o nvt_vis.tpr > gromppout 2>> gromppout
-#gmx mdrun -table "$output_path"/MCMC_"$iMCMC"/tab_it.xvg -pin on -pinoffset "$pinoffset" -pinstride 1 -nt "$nt_vis" -nb cpu -deffnm nvt_vis > runout 2>> runout & #Can use more cores in liquid phase since vapor phase will have already finished
-gmx mdrun -table "$output_path"/MCMC_"$iMCMC"/tab_it.xvg -nt "$nt_vis" -nb cpu -pme cpu -deffnm nvt_vis -o nvt_vis.trr > runout 2>> runout &
-#gmx mdrun -table "$output_path"/MCMC_"$iMCMC"/tab_it.xvg -nt "$nt_vis" -nb cpu -deffnm nvt_vis > runout 2>> runout &
-taskset -cp "$pinoffset"-"$((pinoffset+nt_vis-1))" $! > /dev/null 2>&1
-
-pinoffset=$((pinoffset+nt_vis))
-
-done #for iMCMC
-
-
-echo Waiting for "$Conditions_type" viscosities
-
-nit=0
-maxit=3000000
-ndone=$(cat "$output_path"/MCMC_*/Saturated/rho"$j"/Rep"$nRep"/NVT_eq/NVT_prod/NVT_vis/runout | grep -c "GROMACS reminds you")
-while [ $ndone -lt $((NREP_high+1)) ] && [ $nit -lt $maxit ]
-do
-nit=$((nit+1))
-sleep 100s #00s 
-echo Waiting for "$Conditions_type" viscosities
-ndone=$(cat "$output_path"/MCMC_*/Saturated/rho"$j"/Rep"$nRep"/NVT_eq/NVT_prod/NVT_vis/runout | grep -c "GROMACS reminds you")
-done
-
-###Data analysis
-
-### Uncomment this to have jobs stop half way through. This allows the data analysis to use fewer cores if the output files are enormous.
-#bash "$scripts_path"/recompile_output
-#exit 0
-
-echo "Waiting for post processing viscosity data"
-
-if [ "$NEMD" = "YES" ]
-then
-echo "Processing for NEMD"
-for iMCMC in $(seq $NREP_low $NREP_high)
-do
-cd "$output_path"/MCMC_"$iMCMC"/Saturated/rho"$j"/Rep"$nRep"/NVT_eq/NVT_prod/NVT_vis || error_report "Unable to change to NVT_vis" "$j" "$iMCMC" "post processing"  #start fresh for do cycle instead of multiple "cd .."'s
-echo 34 | gmx energy -f nvt_vis.edr -s nvt_vis.tpr > vis_out 2 >> vis_out   # Get 1/NEMD_VISCOSITY
-awk -f "$scripts_path"/vis_arrange.awk < energy.xvg > visco_temp.xvg  # Convert to NEMD_VISCOSITY
-awk -f "$scripts_path"/runavg.awk < visco_temp.xvg > visco.xvg  # Perform running average
-vis_avg=$(<visco_avg.txt)  # Read in average
-echo "${cos_acc[iMCMC]}	$vis_avg" >> "$output_path"/cosacc_vs_vis.txt
-rm visco_temp.xvg  # Remove bulky files
-rm energy.xvg
-done
-exit 0
-else
-
-for iMCMC in $(seq $NREP_low $NREP_high)
-do
-
-cd "$output_path"/MCMC_"$iMCMC"/Saturated/rho"$j"/Rep"$nRep"/NVT_eq/NVT_prod/NVT_vis || error_report "Unable to change to NVT_vis" "$j" "$iMCMC" "post processing"  #start fresh for do cycle instead of multiple "cd .."'s
-
-# Don't need trajectories of eq and prod with viscosity
-# Modified .mdp so that trajectories are not produced, i.e. this is no longer needed
-#rm ../nvt_prod.trr
-#rm ../../nvt_eq.trr
-
-### Analyze trajectories for TCAF method
-# No longer using TCAF to obtain viscosities
-#echo 0 | gmx tcaf -f nvt_vis.trr -s nvt_vis.tpr > tcaf_out 2>> tcaf_out &
-
-Lbox="${liquid_box[j]}"
-if [ "$NPT" = "YES" ]  # If necessary, fetch the box size used due to NPT equilibration
-then
-Lbox=$(<../../../NPT_eq/NPT_prod/Lbox_NPT_ave)
-fi
-Vbox=$(echo $Lbox|awk '{print $1*$1*$1}')
-echo "Using Lbox $Lbox and Vbox $Vbox in post processing MCMC $iMCMC j $j Rep $nRep"
-
-### Analyze Green-Kubo and Einstein
-
-echo "$Vbox" | gmx energy -f nvt_vis.edr -s nvt_vis.tpr -vis > vis_out 2>> vis_out &
-ls -la >> size_records.txt
-
-done #for iMCMC
-
-nit=0
-maxit=60000 #Don't want this too high, so it will finish eventually
-ndone=$(cat "$output_path"/MCMC_*/Saturated/rho"$j"/Rep"$nRep"/NVT_eq/NVT_prod/NVT_vis/vis_out | grep -c "GROMACS reminds you")
-while [ $ndone -lt $((NREP_high+1)) ] && [ $nit -lt $maxit ]
-do
-nit=$((nit+1))
-sleep 10s
-echo "Still post processing viscosity data"
-ndone=$(cat "$output_path"/MCMC_*/Saturated/rho"$j"/Rep"$nRep"/NVT_eq/NVT_prod/NVT_vis/vis_out | grep -c "GROMACS reminds you")
-done
-
-fi  # If statement for what to do in case of NEMD vs EMD
-
-sleep 10s  # Added in because large files take time to finalize/move/copy
-
-if [ "$RDF" = "YES" ]  # An RDF calculation has been requested
-then
-echo "Working on RDF's"
-# Switch into every directory and perform RDF
-for iMCMC in $(seq $NREP_low $NREP_high)
-do
-# Should we actually operate on this iMCMC?
-if [ "$RDF_single" != "YES" ] || [ "$iMCMC" -eq 0 ]
-then
-cd "$output_path"/MCMC_"$iMCMC"/Saturated/rho"$j"/Rep"$nRep"/NVT_eq/NVT_prod/NVT_vis || exit  #start fresh for do cycle instead of multiple "cd .."'s
-for i in $(seq 0 $rdf_lim)
-do
-# Name a file and run the requested rdf; there may be several
-filename=${refs[i]}_v_${sels[i]}_rdf 
-gmx rdf -f nvt_vis.trr -s nvt_vis.tpr -n ../../../index.ndx -ref ${refs[i]} -sel ${sels[i]} -o "$filename" -cut "$cut_rdf" >rdfout 2>>rdfout
-gracebat -hdevice PNG "$filename".xvg >/dev/null 2>/dev/null
-done  # With all requested RDFs
-fi    # With decision of whether to operate this round
-done  # With all iMCMC rdf runs
-fi # if RDF=YES
-
-echo "Removing large viscosity output files"
-
-for iMCMC in $(seq $NREP_low $NREP_high)
-do
-
-cd "$output_path"/MCMC_"$iMCMC"/Saturated/rho"$j"/Rep"$nRep"/NVT_eq/NVT_prod/NVT_vis || error_report "Unable to change to NVT_vis directory" "$j" "$iMCMC" "post processing"  #start fresh for do cycle instead of multiple "cd .."'s
-
-if [ -e vis_out ]
-then
-echo "Second attempt at size info gathering" > size_records.txt
-ls -la >> size_records.txt
-rm nvt_vis.trr
-rm energy.xvg
-rm nvt_vis.edr
-rm enecorr.xvg
-rm -f \#*
-else
-echo WARNING: No vis_out file for "$output_path"/MCMC_"$iMCMC"/Saturated/rho"$j"/Rep"$nRep" >> "$output_path"/warnings_job_"$job_date"
-fi
-
-
-### Compile the pressure values; Due to different storage for the bond types, requires nested ifs
-if [ "$BondType" = harmonic ]
-then
-
-if [ "$Compound" = Ethane ]
-then
-sed -e '1,/A V E R A G E S/d' nvt_vis.log | grep -m 1 -A1 'Pressure' | tail -n 1 | awk '{print $1}' > press_log
-elif [ "$Compound" = C3H8 ] || [ "$Compound" = IC4H10 ] || [ "$Compound" = NEOC5H12 ]
-then
-sed -e '1,/A V E R A G E S/d' nvt_vis.log | grep -m 1 -A1 'Pressure' | tail -n 1 | awk '{print $2}' > press_log
-else
-sed -e '1,/A V E R A G E S/d' nvt_vis.log | grep -m 1 -A1 'Pressure' | tail -n 1 | awk '{print $3}' > press_log
-fi
-
-else
-
-if [ "$Compound" = Ethane ]
-then
-sed -e '1,/A V E R A G E S/d' nvt_vis.log | grep -m 1 -A1 'Pressure' | tail -n 1 | awk '{print $5}' > press_log
-elif [ "$Compound" = C3H8 ] || [ "$Compound" = IC4H10 ] || [ "$Compound" = NEOC5H12 ]
-then
-sed -e '1,/A V E R A G E S/d' nvt_vis.log | grep -m 1 -A1 'Pressure' | tail -n 1 | awk '{print $1}' > press_log
-else
-sed -e '1,/A V E R A G E S/d' nvt_vis.log | grep -m 1 -A1 'Pressure' | tail -n 1 | awk '{print $2}' > press_log
-fi
-fi
-
-cat "$output_path"/press_all_log press_log > "$output_path"/press_all_temp
-cp "$output_path"/press_all_temp "$output_path"/press_all_log
-rm "$output_path"/press_all_temp
-###
-
-if [ "$NPT" = "YES" ]  # Then we should fetch the box sizes...
-then
-### Compile the box sizes
-cd "$output_path"/MCMC_"$iMCMC"/Saturated/rho"$j"/Rep"$nRep"/NPT_eq/NPT_prod || error_report "Unable to change to NPT_prod directory" "$j" "$iMCMC" "post processing" 
-cat "$output_path"/Lbox_all Lbox_NPT_ave > "$output_path"/Lbox_all_temp
-cp "$output_path"/Lbox_all_temp "$output_path"/Lbox_all
-rm "$output_path"/Lbox_all_temp
-fi
-
-done #for iMCMC
-
-
-cd "$output_path"/MCMC_"$iMCMC"/Saturated || error_report "Unable to change to Saturated directory" "$j" "$iMCMC" "post processing" 
-
-#rm -f rho"$j"/Rep"$nRep"/NVT_eq/NVT_prod/NVT_vis/tcaf_all.xvg
-
-NREP_low=$((NREP_low+NREPS))
-NREP_high=$((NREP_high+NREPS))
-
-echo iRep = "$iRep"
-echo NREP_low = "$NREP_low"
-echo NREP_high = "$NREP_high"
-
-done # for iRep
-
-cd "$output_path" || error_report "Unable to change to $output_path directory" "$j" "$iMCMC" "post processing" 
-echo "In $PWD"
-
-###GreenKubo_analyze for all MCMC parameter sets
-python "$scripts_path"/GreenKubo_analyze.py --ilow 0 --ihigh $((NREP_low-1)) --nReps 1 --irho "$j" --sat
-
-done  # For each j
-
-cd "$output_path" || error_report "Unable to change to $output_path directory" "$j" "$iMCMC" "post processing" 
-###Create plots to compare with experimental data and correlations
-if [ "$Conditions_type" = "Saturation" ]
-then
-python "$scripts_path"/compare_TDE_REFPROP.py --comp "$Compound" --nrhomax $((j+1)) --sat
-else
-python "$scripts_path"/compare_TDE_REFPROP.py --comp "$Compound" --nrhomax $((j+1)) --"$Conditions_type"
-fi
-
-exit 0
-
-#######
-
+#!/bin/bash
+source /usr/local/gromacs/bin/GMXRC
+####
+#
+#This code submits a set of CH3 and CH2 parameter sets (determined by Bayesian MCMC with a different code)
+#Simulations are performed at 5 conditions read from files.
+#Temperatures are performed sequentially, batches of NREPS parameter sets are submitted at a time
+#Green-Kubo analysis is used after each temperature loop is completed
+#
+#
+####
+
+### IN ORDER TO CALCULATE RDF FUNCTIONS:
+# The groups specified by refs and sels (see below)
+# must be specified in the original compound's .gro file
+# Check that the names given in the .gro file are the names
+# which actually appear in the index file if there are problems.
+# Trajectory files must exists for the NVT production run
+###
+
+### IN ORDER TO RUN NEMD
+# 
+###
+
+# Gives a more informative error when something goes wrong
+# with the script.
+error_report() {
+echo "Error $1 on j $2, iMCMC $3, stage $4"
+exit 1
+}
+
+clean() {   # Make it so everything is killed on an interrupt
+local pids=$(jobs -pr)
+echo "On exit sending kill signal to: $pids"
+[ -n "$pids" ] && kill $pids
+exit 1
+}
+trap "clean" SIGINT SIGTERM EXIT SIGQUIT  # Call cleanup when asked to
+
+job_date=$(date "+%Y_%m_%d_%H_%M_%S")
+
+Compound=224TMHexane
+Model=Potoff
+Conditions_type=T293highP    #Saturation         #"$Model"_Saturation   #Saturation # ie T293highP
+BondType=LINCS  #Harmonic (flexible) or LINCS (fixed)
+Temp=293  # Default temp, used if no temperature file is found in conditions path
+jlim=13  # Upper bound on j; condition sets to run; exclusive. Should usually be 5
+jlow=12  # Lower bound on j; inclusive. needed in special cases. Should usually be 0
+batches=3  # Number of batches to run
+NREPS=20 #Run NREPS replicates in parallel/# in a batch (Overriden by NEMD=YES)
+pin0=0  # Default pinoffset, used to tell taskset where to run jobs
+nt_eq=1  # Thread number during equilibration
+nt_vis=1  # This thread number will serve in production and viscosity runs
+NPT=NO # YES indicates NPT runs should be carried out prior to NVT runs (YES or NO)
+#echo "CHANGE THIS BACK BEFORE RUNNING MORE T293highP!!!"
+NEMD=NO  # Calculate viscosity using the periodic perturbation method  (YES or NO)
+RDF=NO  # Whether to perform RDF calculations (YES or NO)
+MCMC_tors=NO # YES indicates model includes torsional uncertainties
+#Set the number of molecules
+Nmol=200
+
+
+###### STEP SIZE INFORMATION #######
+# Runtiming control: override default runtimes=YES, otherwise use NO
+OVERRIDE_STEPS=YES
+# If OVERRIDE_STEPS=YES, arrays must be of length j 
+# indicating how many equilibration and production steps,
+# respectively, to perform for each j
+#equil_steps=(500000 500000 500000 500000 500000)
+#prod_steps=(500000 500000 500000 500000 500000)
+equil_steps=(500000 500000 500000 500000 500000 500000 500000 500000 500000 500000 500000 500000 500000)
+prod_steps=(500000 500000 500000 500000 500000 1000000 2000000 4000000 4000000 8000000 8000000 12000000 48000000)
+
+# The mdp path is decided later based on the kind of run, but in the case that Lennard Jones
+# mdp's will be used, the lj_mdp_path will be the variable selected, otherwise t_mdp_path will be used.
+lj_mdp_path=~/LennardJones
+t_mdp_path=~/Tabulated
+
+#### RDF INFORMATION #####
+RDF_single=NO   # Only perform one RDF run for each j (YES or NO)
+rdfs=2  # Number of RDF functions to produce for each NVT production run
+refs=(H2 H3)  # The references for RDF computation; length must equal rdfs
+sels=(H2 H3)  # The other group in the RDF computation
+cut_rdf=.2  # Cutoff for interactions calculated by RDF
+
+#### NEMD INFORMATION #######
+if [ "$NEMD" = "YES" ]
+then
+NEMD_pts=10  # Number of different cos-accelerations to use
+cos_acc=(.01 .02 .03 .04 .05 .06 .07 .08 .09 .1)
+NREPS=$NEMD_pts
+fi
+
+#Specify the path location for files
+scripts_path=~/Scripts
+conditions_path=~/"$Conditions_type"_Conditions  
+exp_data_path=~/TDE_REFPROP_values
+input_path=~/"$Compound"/Gromacs/Gromacs_input
+if [ "$NEMD" = "YES" ]
+then
+output_path=~/"$Compound"/Gromacs/"$Conditions_type"_Viscosity/"$Model"_N"$Nmol"_"$BondType"_NEMD #Code assumes that a folder already exists with this directory and the eps_sig_lam_MCMC file in it
+else
+output_path=~/"$Compound"/Gromacs/"$Conditions_type"_Viscosity/"$Model"_N"$Nmol"_"$BondType" 
+fi
+
+if [ "$MCMC_tors" = "YES" ]
+then
+output_path="$output_path"_MCMC_tors
+echo "Using MCMC derived torsional parameters"
+
+else
+
+echo "Using fixed literature values for torsional parameters"
+
+fi
+
+jobfile="$output_path"/"$Compound"_job_"$job_date" 
+cp "$scripts_path"/AlkanesViscosity.sh "$jobfile" #Keep track of what jobs have been submitted
+cat "$scripts_path"/nAlkanesNPTsteps >> "$jobfile"  # Inellegant append
+cat "$scripts_path"/run_single.sh >> "$jobfile"  # Another inellegant append
+touch "$output_path"/warnings_job_"$job_date"
+
+cd "$output_path" || error_report "Error switching to $output_path" "0" "0" "preprocessing"
+
+touch press_all_log
+touch Lbox_all
+
+### Read the box size, that depends on number of molecules
+if [ -f "$conditions_path"/"$Compound"_liquid_box_N"$Nmol" ]
+then
+
+while read line
+do 
+liquid_box+=("$line")
+done < "$conditions_path"/"$Compound"_liquid_box_N"$Nmol"
+
+else
+echo "Unable to read box from $conditions_path"/"$Compound"_liquid_box_N"$Nmol"
+exit 1
+fi
+
+# If pressure data is needed for an NPT run,
+# Determine whether or not the pressure data is available.
+if [ "$NPT" = "YES" ]
+then
+if [ -f "$conditions_path"/"$Compound"_press ]
+then
+echo Pressures ${press[@]} read from "$conditions_path"/"$Compound"_press
+else
+echo Pressures could not be read from "$conditions_path"/"$Compound"_press
+exit 1
+fi
+
+### Read the pressure file into the array 'press'
+while read line
+do
+press+=("$line")
+done < "$conditions_path"/"$Compound"_press
+fi
+
+### Determine Temperature. In some cases temperature should be read from a file
+# IF a temperature file exists, it will use that 
+temp_search_path="$conditions_path"/"$Compound"_Temp
+if [ "$Conditions_type" = "Saturation" ] || [ "$Conditions_type" = "$Model"_"Saturation" ]
+then
+temp_search_path="$conditions_path"/"$Compound"_Tsat
+fi
+echo Looking for temperatures at "$temp_search_path"
+if [ -e "$temp_search_path" ]
+then
+while read line
+do 
+temps+=("$line")
+done < "$temp_search_path"
+
+# Otherwise, fill the array with copies of the given temperature
+# Make the array the same length as the pressure
+echo Temperatures ${temps[@]} read from "$temp_search_path"
+else
+for ((x=0; x < ${#liquid_box[@]}; x++))  # C style loop 
+do
+temps+=("$Temp")
+done
+echo Temperatures ${temps[@]} from default temperature used
+fi
+
+###Equilibration time is different for certain compounds
+# 0.002 ps time step
+
+if [ "$Compound" = 'C3H8' ]
+then
+
+nsteps_eq=50000 # 0.1 ns total
+
+elif [ "$Compound" = 'C4H10' ]
+then
+
+nsteps_eq=100000 # 0.2 ns total
+
+else
+
+nsteps_eq=500000 # 1 ns total
+
+fi
+
+# We're going to ignore normal step sizes
+if [ "$OVERRIDE_STEPS" = "YES" ]
+then
+echo Overriding step numbers using equil=${equil_steps[*]}, prod=${prod_steps[*]}
+# Use predefined step sizes
+else
+for ((x=0; x < jlim; x++))
+do
+equil_steps[$x]=$nsteps_eq
+prod_steps[$x]=500000
+done
+fi
+echo Step numbers : equil=${equil_steps[*]}, prod=${prod_steps[*]}
+
+
+###Cut-off distance is different for some force fields
+if [ "$Model" = 'Potoff' ]
+then
+
+rvdw=1.0 # [nm]
+
+else
+
+rvdw=1.4 # [nm]
+
+fi
+
+### Assign force field parameters
+if [ "$Model" = 'TraPPE' ]
+then
+
+#TraPPE
+
+bondlength_CH3=0.1540
+
+epsCH3_sim=98. # (K)
+sigCH3_sim=0.375 # (nm)
+lamCH3_sim=12.0
+
+epsCH2_sim=46. # (K)
+sigCH2_sim=0.395 # (nm)
+lamCH2_sim=12.0
+
+epsCH_sim=10. # (K)
+sigCH_sim=0.468 # (nm)
+lamCH_sim=12.0
+
+epsC_sim=0.5 # (K)
+sigC_sim=0.640 # (nm)
+lamC_sim=12.0
+
+lam_sim=12.0
+
+elif [ "$Model" = 'TraPPEAUA' ]
+then
+
+#TraPPE_AUA
+
+bondlength_CH3=0.192
+
+epsCH3_sim=134.5 # (K)
+sigCH3_sim=0.352 # (nm)
+lamCH3_sim=12.0
+
+#Borrow the rest from TraPPE-UA
+
+epsCH2_sim=46. # (K)
+sigCH2_sim=0.395 # (nm)
+lamCH2_sim=12.0
+
+epsCH_sim=10. # (K)
+sigCH_sim=0.468 # (nm)
+lamCH_sim=12.0
+
+epsC_sim=0.5 # (K)
+sigC_sim=0.640 # (nm)
+lamC_sim=12.0
+
+lam_sim=12.0
+
+elif [ "$Model" = 'Potoff' ]
+then
+
+#Potoff
+
+bondlength_CH3=0.1540
+
+epsCH3_sim=121.25 # (K)
+sigCH3_sim=0.3783 # (nm)
+lamCH3_sim=16.0
+
+epsCH2_sim=61. # (K)
+sigCH2_sim=0.399 # (nm)
+lamCH2_sim=16.0
+
+#S/L
+if [ "$Compound" = 'IC4H10' ] || [ "$Compound" = 'IC5H12' ] || [ "$Compound" = 'NEOC5H12' ] || [ "$Compound" = '23DMButane' ]
+then
+
+#Short (4 or fewer C backbone)
+epsCH_sim=15.00 # (K)
+sigCH_sim=0.470 # (nm)
+lamCH_sim=16.0
+
+epsC_sim=1.45 # (K)
+sigC_sim=0.610 # (nm)
+lamC_sim=16.0
+
+echo "You are using short CH and C parameters"
+
+elif [ "$Compound" = 'IC6H14' ] || [ "$Compound" = 'IC8H18' ] || [ "$Compound" = '3MPentane' ] || [ "$Compound" = '224TMHexane' ]
+then
+
+#Long (5 or more C backbone)
+epsCH_sim=14.00 # (K)
+sigCH_sim=0.470 # (nm)
+lamCH_sim=16.0
+
+epsC_sim=1.2 # (K)
+sigC_sim=0.620 # (nm)
+lamC_sim=16.0
+
+echo "You are using long CH and C parameters"
+
+else
+
+# Transferable sites
+epsCH_sim=15.00 # (K)
+sigCH_sim=0.460 # (nm)
+lamCH_sim=16.0
+
+epsC_sim=0.5 # (K)
+sigC_sim=0.610 # (nm)
+lamC_sim=16.0
+
+echo "You are using transferable CH and C parameters"
+
+fi
+
+lam_sim=16.0
+
+elif [ "$Model" = 'TAMie' ]
+then
+
+#TAMie
+
+bondlength_CH3=0.174
+
+epsCH3_sim=136.318 # (K)
+sigCH3_sim=0.36034 # (nm)
+lamCH3_sim=14.0
+
+epsCH2_sim=52.9133 # (K)
+sigCH2_sim=0.404 # (nm)
+lamCH2_sim=14.0
+
+epsCH_sim=14.5392 # (K)
+sigCH_sim=0.43656 # (nm)
+lamCH_sim=14.0
+
+epsC_sim=0.0 # (K)
+sigC_sim=0.0 # (nm)
+lamC_sim=14.0
+
+lam_sim=14.0
+
+elif [ "$Model" = 'AUA4' ]
+then
+
+#AUA4
+
+if [ "$Compound" = 'C2H6' ]
+then
+
+bondlength_CH3=0.196668
+
+else
+
+bondlength_CH3=0.1751
+
+fi
+
+epsCH3_sim=120.15 # (K)
+sigCH3_sim=0.36072 # (nm)
+lamCH3_sim=12.0
+
+epsCH2_sim=86.29 # (K)
+sigCH2_sim=0.3431 # (nm)
+lamCH2_sim=12.0
+
+epsCH_sim=50.98 # (K)
+sigCH_sim=0.3363 # (nm)
+lamCH_sim=12.0
+
+epsC_sim=15.04 # (K)
+sigC_sim=0.244 # (nm)
+lamC_sim=12.0
+
+lam_sim=12.0
+
+#Standard CC bondlength for AUA4 = 0.1535 nm
+#delta_CH3=0.0216 nm
+#delta_CH2=0.0384 nm
+#delta_CH=0.0646 nm
+
+else
+
+bondlength_CH3=0.154 #(nm)
+
+fi
+
+if [ "$lam_sim" = 12.0 ]
+then
+
+echo "Using native Lennard-Jones potential"
+mdp_path="$lj_mdp_path"
+#Originally I tried to have a tab_flag variable, but it was not working for tabulated because
+#using "$tab_flag" in mdrun was different than echo. Fortunately, I discovered that Gromacs
+#will just ignore the provided table if the vdwtype is cut-off instead of user.
+#tab_flag=""
+
+else
+
+echo "Using tabulated potential"
+mdp_path="$t_mdp_path"
+#This also required copying tab_it into the output_path whereas it is typically output_path/MCMC_iMCMC
+#tab_flag="-table $output_path/tab_it.xvg "
+
+fi
+
+### Copy experimental data files to output directory
+
+# Copy in appropriate data for later post processing
+if [ "$Conditions_type" = "Saturation" ]
+then
+cp "$exp_data_path"/"$Compound"_TDE_eta_sat.txt "$output_path"/TDE_eta_sat.txt
+cp "$exp_data_path"/"$Compound"_REFPROP_eta_sat.txt "$output_path"/REFPROP_eta_sat.txt
+else
+cp "$exp_data_path"/"$Compound"_REFPROP_eta_"$Conditions_type".txt "$output_path"/REFPROP_eta_"$Conditions_type".txt
+fi
+
+
+### Create file and header for state point conditions if not already created
+if [ ! -e "$output_path"/"$Conditions_type"Settings.txt ]
+then
+echo "NMol" "Length (nm)" "Temp (K)" > "$output_path"/"$Conditions_type"Settings.txt	
+fi
+
+### Loop through temperatures and densities		
+jlim=$((jlim - 1))
+batches=$((batches - 1))  # Limits for 0 indexed loops later
+
+for j in $(seq $jlow $jlim) # Number of conditions to run
+
+do
+
+### Record state points
+echo "$Nmol" "${liquid_box[j]}" "${temps[j]}" >> "$output_path"/"$Conditions_type"Settings.txt
+
+nRep=0
+
+NREP_low=0
+NREP_high=$((NREPS-1))
+
+#NREP_low=$((NREP_low+20+15))
+#NREP_high=$((NREP_high+20+15))
+
+####
+
+for iRep in $(seq 0 $batches) # Number of batches to run (0 9), 10 batches with 20 replicates is 200 parameter sets
+
+do
+
+for iMCMC in $(seq $NREP_low $NREP_high)
+do
+
+cd "$output_path" || error_report "Unable to change to $output_path" "$j" "$iMCMC" "start up" 
+
+### Read in eps, sig, and lam from a file that contains the MCMC samples
+
+if [ "$Model" = 'MCMC_lam16' ]
+then
+
+epsCH3_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print $1}' < ~/MCMC_parameter_sets/eps_sig_lam16_MCMC_CH3_CH2_CH_C)
+sigCH3_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print $2}' < ~/MCMC_parameter_sets/eps_sig_lam16_MCMC_CH3_CH2_CH_C)
+lam_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print $3}' < ~/MCMC_parameter_sets/eps_sig_lam16_MCMC_CH3_CH2_CH_C)
+epsCH2_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print $4}' < ~/MCMC_parameter_sets/eps_sig_lam16_MCMC_CH3_CH2_CH_C)
+sigCH2_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print $5}' < ~/MCMC_parameter_sets/eps_sig_lam16_MCMC_CH3_CH2_CH_C)
+epsCH_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print $7}' < ~/MCMC_parameter_sets/eps_sig_lam16_MCMC_CH3_CH2_CH_C)
+sigCH_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print $8}' < ~/MCMC_parameter_sets/eps_sig_lam16_MCMC_CH3_CH2_CH_C)
+epsC_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print $10}' < ~/MCMC_parameter_sets/eps_sig_lam16_MCMC_CH3_CH2_CH_C)
+sigC_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print $11}' < ~/MCMC_parameter_sets/eps_sig_lam16_MCMC_CH3_CH2_CH_C)
+
+fi
+
+#if [ "$MCMC_tors" = "YES" ]
+#then
+#
+#CH2_CH2_tors_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print $1}' < ~/MCMC_parameter_sets/MCMC_CH2_CH2_tors)
+#CH2_CH_tors_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print $2}' < ~/MCMC_parameter_sets/MCMC_CH2_CH_tors)
+#CH2_C_tors_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print $3}' < ~/MCMC_parameter_sets/MCMC_CH2_C_tors)
+#CH_CH_tors_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print $4}' < ~/MCMC_parameter_sets/MCMC_CH_CH_tors)
+#
+#fi
+
+echo iMCMC = "$iMCMC"
+
+echo Run "$Conditions_type" Viscosity for epsCH3 = "$epsCH3_sim" sigCH3 = "$sigCH3_sim" lamCH3 = "$lam_sim" epsCH2 = "$epsCH2_sim" sigCH2 = "$sigCH2_sim" lamCH2 = "$lam_sim" epsCH = "$epsCH_sim" sigCH = "$sigCH_sim" lamCH = "$lam_sim" epsC = "$epsC_sim" sigC = "$sigC_sim" lamC = "$lam_sim"
+
+####
+
+mkdir -p MCMC_"$iMCMC"
+cd MCMC_"$iMCMC" || error_report "Unable to change to MCMC_$iMCMC" "$j" "$iMCMC" "start up"
+
+###Create files with force field parameters
+bash "$scripts_path"/force_field_params "$Compound" "$input_path" "$scripts_path" "$lam_sim" "$epsCH3_sim" "$sigCH3_sim" "$epsCH2_sim" "$sigCH2_sim" "$epsCH_sim" "$sigCH_sim" "$epsC_sim" "$sigC_sim" "$bondlength_CH3" "$Nmol" "$MCMC_tors" "$iMCMC"  #"${CH2_CH2_tors_sim[@]}" "${CH2_CH_tors_sim[@]}" "${CH2_C_tors_sim[@]}" "${CH_CH_tors_sim[@]}"
+
+### Copy tab_it.xvg to previous directory, assumes that all MCMC parameter sets use the same value of lambda
+#Not needed anymore
+#cp tab_it.xvg ../tab_it.xvg
+
+### Record state points, include header if creating file
+### Moved this outside of loop
+#if [ -e "$output_path"/MCMC_"$iMCMC"/"$Conditions_type"Settings.txt ]
+#then
+#echo "NMol" "Length (nm)" "Temp (K)" > "$output_path"/MCMC_"$iMCMC"/"$Conditions_type"Settings.txt
+#fi
+
+# Initialize the folders, copy files, and insert variables
+
+cd "$output_path"/MCMC_"$iMCMC" || error_report "Unable to change to directory MCMC_$iMCMC" "$j" "$iMCMC" "start up"  #presumes this dir was made previously
+
+mkdir -p Saturated
+cd Saturated || error_report "Unable to change to directory Saturated" "$j" "$iMCMC" "start up" 
+
+mkdir -p rho"$j"
+cd    rho"$j" || error_report "Unable to change to directory rho$j" "$j" "$iMCMC" "start up"
+
+#echo "$Nmol" "${liquid_box[j]}" "${Temp}" >> "$output_path"/MCMC_"$iMCMC"/"$Conditions_type"Settings.txt
+
+mkdir -p Rep"$nRep"  
+cd    Rep"$nRep" || error_report "Unable to change to directory Rep$nRep" "$j" "$iMCMC" "start up"
+
+gmx insert-molecules -ci ../../../"$Compound".gro -nmol "$Nmol" -try 2000 -box "${liquid_box[j]}" "${liquid_box[j]}" "${liquid_box[j]}" -o "$Compound"_box.gro > insertout 2>> insertout
+
+if [ "$RDF" = "YES" ]  # Do RDF setup
+then
+rdf_lim=$((rdfs - 1))  # Will be needed later for RDF computational loop
+# Create the index file for later- pipes the necessary quit command to the interactive tool
+echo q | gmx make_ndx -f "$Compound"_box.gro -o index.ndx > make_ndx.out 2>> make_ndx.out  
+fi
+
+#Copy the minimization files
+echo mdp_path "$mdp_path"
+cp "$mdp_path"/em_steep.mdp em_steep.mdp
+cp "$mdp_path"/em_l-bfgs.mdp em_l-bfgs.mdp
+
+sed -i -e s/some_rvdw/"$rvdw"/ em_steep.mdp
+sed -i -e s/some_rvdw/"$rvdw"/ em_l-bfgs.mdp
+
+mkdir -p NVT_eq
+cd NVT_eq || error_report "Unable to change to directory NVT_eq" "$j" "$iMCMC" "start up"
+
+# Copy the equilibration files and edit the temperature
+
+cp "$mdp_path"/nvt_eq_no_output_"$BondType".mdp nvt_eq.mdp
+sed -i -e s/some_temperature/"${temps[j]}"/ nvt_eq.mdp
+sed -i -e s/some_nsteps/"${equil_steps[j]}"/ nvt_eq.mdp
+sed -i -e s/some_rvdw/"$rvdw"/ nvt_eq.mdp
+cur_ind=$((iMCMC - NREP_low))  # Find the proper cos_acceleration and subsitute
+sed -i -e s/some_cos_acceleration/"${cos_acc[cur_ind]}"/ nvt_eq.mdp
+
+# Still creating NVT_prod directory so that our codes are backwards compatible with data analysis (i.e. same directory hierarchy)
+
+mkdir -p NVT_prod
+cd NVT_prod || error_report "Unable to change to directory NVT_prod" "$j" "$iMCMC" "start up"
+# Create new directory for viscosity run
+
+mkdir -p NVT_vis
+cd NVT_vis || error_report "Unable to change to directory NVT_vis" "$j" "$iMCMC" "start up"
+
+# Copy the viscosity files and edit the temperature
+
+cp "$mdp_path"/nvt_vis_no_xv_"$BondType".mdp nvt_vis.mdp
+sed -i -e s/some_temperature/"${temps[j]}"/ nvt_vis.mdp
+sed -i -e s/some_nsteps/"${prod_steps[j]}"/ nvt_vis.mdp
+sed -i -e s/some_rvdw/"$rvdw"/ nvt_vis.mdp
+sed -i -e s/some_cos_acceleration/"${cos_acc[cur_ind]}"/ nvt_vis.mdp
+
+done # for loop over iMCMC
+
+### Run the NPT steps to determine the box sizes
+# Skip this if NPT != YES
+if [ "$NPT" = "YES" ]
+then
+bash "$scripts_path"/nAlkanesNPTsteps "$Compound" "$Nmol" "${liquid_box[j]}" "$mdp_path" "$BondType" "${temps[j]}" "${press[j]}" "${equil_steps[j]}" "$rvdw" "$NREP_low" "$NREP_high" "$output_path" "$j" "$nRep" "$scripts_path" "$pin0" "$nt_eq" "$nt_vis" "${prod_steps[j]}"
+fi
+
+###First energy minimization
+
+pinoffset=$pin0
+
+for iMCMC in $(seq $NREP_low $NREP_high)
+do
+
+echo pinoffset = "$pinoffset"
+
+cd "$output_path"/MCMC_"$iMCMC"/Saturated/rho"$j"/Rep"$nRep" || exit  #start fresh for do cycle instead of multiple "cd .."'s
+
+gmx grompp -f em_steep.mdp -c "$Compound"_box.gro -p ../../../"$Compound".top -o em_steep.tpr > gromppout 2>> gromppout
+#We now use a different approach for assigning nodes
+#gmx mdrun -table "$output_path"/MCMC_"$iMCMC"/tab_it.xvg -pin on -pinoffset "$pinoffset" -pinstride 1 -ntomp 1 -nt 1 -nb cpu -deffnm em_steep > runout 2>> runout &
+gmx mdrun -table "$output_path"/MCMC_"$iMCMC"/tab_it.xvg -nt 1 -nb cpu -pme cpu -deffnm em_steep > runout 2>> runout &
+#gmx mdrun -table "$output_path"/MCMC_"$iMCMC"/tab_it.xvg -nt 1 -nb cpu -deffnm em_steep > runout 2>> runout &
+cur_pid=$!
+taskset -cp "$pinoffset" $cur_pid > /dev/null 2>&1
+min_3_pids[${iMCMC}]=$cur_pid  # This is the third such step (others are in the subscript) hence 3
+
+pinoffset=$((pinoffset+1))
+
+done #for iMCMC
+
+echo "Waiting for em_steep.tpr: Energy Minimization Part1"
+
+for pid in ${min_3_pids[*]}  # Loop over array
+do 
+wait $pid
+done
+
+###Second energy minimization
+
+pinoffset=$pin0
+
+for iMCMC in $(seq $NREP_low $NREP_high)
+do
+
+echo pinoffset = "$pinoffset"
+
+cd "$output_path"/MCMC_"$iMCMC"/Saturated/rho"$j"/Rep"$nRep" || error_report "Unable to change to directory Rep$nRep" "$j" "$iMCMC" "second energy minimzation NVT"  #start fresh for do cycle instead of multiple "cd .."'s
+
+gmx grompp -f em_l-bfgs.mdp -c em_steep.gro -p ../../../"$Compound".top -o em_l_bfgs.tpr -maxwarn 1 >> gromppout 2>> gromppout
+#gmx mdrun -table "$output_path"/MCMC_"$iMCMC"/tab_it.xvg -pin on -pinoffset "$pinoffset" -pinstride 1 -ntomp 1 -nt 1 -nb cpu -deffnm em_l_bfgs >> runout2 2>> runout2 &
+gmx mdrun -table "$output_path"/MCMC_"$iMCMC"/tab_it.xvg -nt 1 -nb cpu -pme cpu -deffnm em_l_bfgs > runout2 2>> runout2 &
+#gmx mdrun -table "$output_path"/MCMC_"$iMCMC"/tab_it.xvg -nt 1 -nb cpu -deffnm em_l_bfgs > runout2 2>> runout2 &
+cur_pid=$!
+taskset -cp "$pinoffset" $cur_pid > /dev/null 2>&1
+min_4_pids[${iMCMC}]=$cur_pid
+
+pinoffset=$((pinoffset+1))
+
+done #for iMCMC
+
+echo "Waiting for second energy minimization"
+
+for pid in ${min_4_pids[*]}  # Iterate over 4th minimization array
+do
+wait $pid
+done
+
+###Equilibration period
+
+pinoffset=$pin0
+
+for iMCMC in $(seq $NREP_low $NREP_high)
+do
+
+echo pinoffset = "$pinoffset"
+
+cd "$output_path"/MCMC_"$iMCMC"/Saturated/rho"$j"/Rep"$nRep"/NVT_eq || error_report "Unable to change to NVT_eq directory" "$j" "$iMCMC" "NVT equilibrium"  #start fresh for do cycle instead of multiple "cd .."'s
+
+if ls ../step*.pdb 1> /dev/null 2>&1 #Remove these warning files
+then
+echo some energy minimizations might have failed for "$output_path"/MCMC_"$iMCMC"/Saturated/rho"$j"/Rep"$nRep" >> "$output_path"/warnings_job_"$job_date"
+rm ../step*.pdb
+fi
+
+gmx grompp -f nvt_eq.mdp -c ../em_l_bfgs.gro -p ../../../../"$Compound".top -o nvt_eq.tpr > gromppout 2>> gromppout
+#gmx mdrun -table "$output_path"/MCMC_"$iMCMC"/tab_it.xvg -pin on -pinoffset "$pinoffset" -pinstride 1 -nt "$nt_eq" -nb cpu -deffnm nvt_eq > runout 2>> runout &
+Tempbox=${liquid_box[j]}  # This is the default for no NPT
+if [ $NPT = YES ]
+then
+Tempbox=$(<../NPT_eq/NPT_prod/Lbox_NPT_ave)  # This is the default for NPT
+fi
+# Pass the proper box size to the subscript in case it needs to restart calculations (it starts from insert molecules)
+bash "$scripts_path"/run_single.sh "$output_path"/MCMC_"$iMCMC"/tab_it.xvg "$nt_eq" cpu cpu nvt_eq "$pinoffset" "$j" "$nRep" "$output_path" "$NREP_low" "$NREP_high" "$Compound" "$Nmol" "$Tempbox" nvt &
+
+pinoffset=$((pinoffset+nt_eq))
+
+done #for iMCMC
+
+echo Waiting for "$Conditions_type" equilibration
+
+nit=0
+maxit=3000000
+ndone=$(cat "$output_path"/MCMC_*/Saturated/rho"$j"/Rep"$nRep"/NVT_eq/runout | grep -c "GROMACS reminds you")
+while [ $ndone -lt $((NREP_high+1)) ] && [ $nit -lt $maxit ]
+do
+nit=$((nit+1))
+sleep 100s 
+echo Waiting for "$Conditions_type" equilibration
+ndone=$(cat "$output_path"/MCMC_*/Saturated/rho"$j"/Rep"$nRep"/NVT_eq/runout | grep -c "GROMACS reminds you")
+done
+
+###Removed production period
+
+###Viscosity period
+
+pinoffset=$pin0
+for iMCMC in $(seq $NREP_low $NREP_high)
+do
+
+echo pinoffset = "$pinoffset"
+
+cd "$output_path"/MCMC_"$iMCMC"/Saturated/rho"$j"/Rep"$nRep"/NVT_eq/NVT_prod/NVT_vis || error_report "Unable to change to directory NVT_vis" "$j" "$iMCMC" "NVT viscosity"  #start fresh for do cycle instead of multiple "cd .."'s
+
+gmx grompp -f nvt_vis.mdp -c ../../nvt_eq.gro -p ../../../../../../"$Compound".top -o nvt_vis.tpr > gromppout 2>> gromppout
+#gmx mdrun -table "$output_path"/MCMC_"$iMCMC"/tab_it.xvg -pin on -pinoffset "$pinoffset" -pinstride 1 -nt "$nt_vis" -nb cpu -deffnm nvt_vis > runout 2>> runout & #Can use more cores in liquid phase since vapor phase will have already finished
+gmx mdrun -table "$output_path"/MCMC_"$iMCMC"/tab_it.xvg -nt "$nt_vis" -nb cpu -pme cpu -deffnm nvt_vis -o nvt_vis.trr > runout 2>> runout &
+#gmx mdrun -table "$output_path"/MCMC_"$iMCMC"/tab_it.xvg -nt "$nt_vis" -nb cpu -deffnm nvt_vis > runout 2>> runout &
+taskset -cp "$pinoffset"-"$((pinoffset+nt_vis-1))" $! > /dev/null 2>&1
+
+pinoffset=$((pinoffset+nt_vis))
+
+done #for iMCMC
+
+
+echo Waiting for "$Conditions_type" viscosities
+
+nit=0
+maxit=3000000
+ndone=$(cat "$output_path"/MCMC_*/Saturated/rho"$j"/Rep"$nRep"/NVT_eq/NVT_prod/NVT_vis/runout | grep -c "GROMACS reminds you")
+while [ $ndone -lt $((NREP_high+1)) ] && [ $nit -lt $maxit ]
+do
+nit=$((nit+1))
+sleep 100s #00s 
+echo Waiting for "$Conditions_type" viscosities
+ndone=$(cat "$output_path"/MCMC_*/Saturated/rho"$j"/Rep"$nRep"/NVT_eq/NVT_prod/NVT_vis/runout | grep -c "GROMACS reminds you")
+done
+
+###Data analysis
+
+### Uncomment this to have jobs stop half way through. This allows the data analysis to use fewer cores if the output files are enormous.
+#bash "$scripts_path"/recompile_output
+#exit 0
+
+echo "Waiting for post processing viscosity data"
+
+if [ "$NEMD" = "YES" ]
+then
+echo "Processing for NEMD"
+for iMCMC in $(seq $NREP_low $NREP_high)
+do
+cd "$output_path"/MCMC_"$iMCMC"/Saturated/rho"$j"/Rep"$nRep"/NVT_eq/NVT_prod/NVT_vis || error_report "Unable to change to NVT_vis" "$j" "$iMCMC" "post processing"  #start fresh for do cycle instead of multiple "cd .."'s
+echo 34 | gmx energy -f nvt_vis.edr -s nvt_vis.tpr > vis_out 2 >> vis_out   # Get 1/NEMD_VISCOSITY
+awk -f "$scripts_path"/vis_arrange.awk < energy.xvg > visco_temp.xvg  # Convert to NEMD_VISCOSITY
+awk -f "$scripts_path"/runavg.awk < visco_temp.xvg > visco.xvg  # Perform running average
+vis_avg=$(<visco_avg.txt)  # Read in average
+echo "${cos_acc[iMCMC]}	$vis_avg" >> "$output_path"/cosacc_vs_vis.txt
+rm visco_temp.xvg  # Remove bulky files
+rm energy.xvg
+done
+exit 0
+else
+
+for iMCMC in $(seq $NREP_low $NREP_high)
+do
+
+cd "$output_path"/MCMC_"$iMCMC"/Saturated/rho"$j"/Rep"$nRep"/NVT_eq/NVT_prod/NVT_vis || error_report "Unable to change to NVT_vis" "$j" "$iMCMC" "post processing"  #start fresh for do cycle instead of multiple "cd .."'s
+
+# Don't need trajectories of eq and prod with viscosity
+# Modified .mdp so that trajectories are not produced, i.e. this is no longer needed
+#rm ../nvt_prod.trr
+#rm ../../nvt_eq.trr
+
+### Analyze trajectories for TCAF method
+# No longer using TCAF to obtain viscosities
+#echo 0 | gmx tcaf -f nvt_vis.trr -s nvt_vis.tpr > tcaf_out 2>> tcaf_out &
+
+Lbox="${liquid_box[j]}"
+if [ "$NPT" = "YES" ]  # If necessary, fetch the box size used due to NPT equilibration
+then
+Lbox=$(<../../../NPT_eq/NPT_prod/Lbox_NPT_ave)
+fi
+Vbox=$(echo $Lbox|awk '{print $1*$1*$1}')
+echo "Using Lbox $Lbox and Vbox $Vbox in post processing MCMC $iMCMC j $j Rep $nRep"
+
+### Analyze Green-Kubo and Einstein
+
+echo "$Vbox" | gmx energy -f nvt_vis.edr -s nvt_vis.tpr -vis > vis_out 2>> vis_out &
+ls -la >> size_records.txt
+
+done #for iMCMC
+
+nit=0
+maxit=60000 #Don't want this too high, so it will finish eventually
+ndone=$(cat "$output_path"/MCMC_*/Saturated/rho"$j"/Rep"$nRep"/NVT_eq/NVT_prod/NVT_vis/vis_out | grep -c "GROMACS reminds you")
+while [ $ndone -lt $((NREP_high+1)) ] && [ $nit -lt $maxit ]
+do
+nit=$((nit+1))
+sleep 10s
+echo "Still post processing viscosity data"
+ndone=$(cat "$output_path"/MCMC_*/Saturated/rho"$j"/Rep"$nRep"/NVT_eq/NVT_prod/NVT_vis/vis_out | grep -c "GROMACS reminds you")
+done
+
+fi  # If statement for what to do in case of NEMD vs EMD
+
+sleep 10s  # Added in because large files take time to finalize/move/copy
+
+if [ "$RDF" = "YES" ]  # An RDF calculation has been requested
+then
+echo "Working on RDF's"
+# Switch into every directory and perform RDF
+for iMCMC in $(seq $NREP_low $NREP_high)
+do
+# Should we actually operate on this iMCMC?
+if [ "$RDF_single" != "YES" ] || [ "$iMCMC" -eq 0 ]
+then
+cd "$output_path"/MCMC_"$iMCMC"/Saturated/rho"$j"/Rep"$nRep"/NVT_eq/NVT_prod/NVT_vis || exit  #start fresh for do cycle instead of multiple "cd .."'s
+for i in $(seq 0 $rdf_lim)
+do
+# Name a file and run the requested rdf; there may be several
+filename=${refs[i]}_v_${sels[i]}_rdf 
+gmx rdf -f nvt_vis.trr -s nvt_vis.tpr -n ../../../index.ndx -ref ${refs[i]} -sel ${sels[i]} -o "$filename" -cut "$cut_rdf" >rdfout 2>>rdfout
+gracebat -hdevice PNG "$filename".xvg >/dev/null 2>/dev/null
+done  # With all requested RDFs
+fi    # With decision of whether to operate this round
+done  # With all iMCMC rdf runs
+fi # if RDF=YES
+
+echo "Removing large viscosity output files"
+
+for iMCMC in $(seq $NREP_low $NREP_high)
+do
+
+cd "$output_path"/MCMC_"$iMCMC"/Saturated/rho"$j"/Rep"$nRep"/NVT_eq/NVT_prod/NVT_vis || error_report "Unable to change to NVT_vis directory" "$j" "$iMCMC" "post processing"  #start fresh for do cycle instead of multiple "cd .."'s
+
+if [ -e vis_out ]
+then
+echo "Second attempt at size info gathering" > size_records.txt
+ls -la >> size_records.txt
+rm nvt_vis.trr
+rm energy.xvg
+rm nvt_vis.edr
+rm enecorr.xvg
+rm -f \#*
+else
+echo WARNING: No vis_out file for "$output_path"/MCMC_"$iMCMC"/Saturated/rho"$j"/Rep"$nRep" >> "$output_path"/warnings_job_"$job_date"
+fi
+
+
+### Compile the pressure values; Due to different storage for the bond types, requires nested ifs
+if [ "$BondType" = harmonic ]
+then
+
+if [ "$Compound" = Ethane ]
+then
+sed -e '1,/A V E R A G E S/d' nvt_vis.log | grep -m 1 -A1 'Pressure' | tail -n 1 | awk '{print $1}' > press_log
+elif [ "$Compound" = C3H8 ] || [ "$Compound" = IC4H10 ] || [ "$Compound" = NEOC5H12 ]
+then
+sed -e '1,/A V E R A G E S/d' nvt_vis.log | grep -m 1 -A1 'Pressure' | tail -n 1 | awk '{print $2}' > press_log
+else
+sed -e '1,/A V E R A G E S/d' nvt_vis.log | grep -m 1 -A1 'Pressure' | tail -n 1 | awk '{print $3}' > press_log
+fi
+
+else
+
+if [ "$Compound" = Ethane ]
+then
+sed -e '1,/A V E R A G E S/d' nvt_vis.log | grep -m 1 -A1 'Pressure' | tail -n 1 | awk '{print $5}' > press_log
+elif [ "$Compound" = C3H8 ] || [ "$Compound" = IC4H10 ] || [ "$Compound" = NEOC5H12 ]
+then
+sed -e '1,/A V E R A G E S/d' nvt_vis.log | grep -m 1 -A1 'Pressure' | tail -n 1 | awk '{print $1}' > press_log
+else
+sed -e '1,/A V E R A G E S/d' nvt_vis.log | grep -m 1 -A1 'Pressure' | tail -n 1 | awk '{print $2}' > press_log
+fi
+fi
+
+cat "$output_path"/press_all_log press_log > "$output_path"/press_all_temp
+cp "$output_path"/press_all_temp "$output_path"/press_all_log
+rm "$output_path"/press_all_temp
+###
+
+if [ "$NPT" = "YES" ]  # Then we should fetch the box sizes...
+then
+### Compile the box sizes
+cd "$output_path"/MCMC_"$iMCMC"/Saturated/rho"$j"/Rep"$nRep"/NPT_eq/NPT_prod || error_report "Unable to change to NPT_prod directory" "$j" "$iMCMC" "post processing" 
+cat "$output_path"/Lbox_all Lbox_NPT_ave > "$output_path"/Lbox_all_temp
+cp "$output_path"/Lbox_all_temp "$output_path"/Lbox_all
+rm "$output_path"/Lbox_all_temp
+fi
+
+done #for iMCMC
+
+
+cd "$output_path"/MCMC_"$iMCMC"/Saturated || error_report "Unable to change to Saturated directory" "$j" "$iMCMC" "post processing" 
+
+#rm -f rho"$j"/Rep"$nRep"/NVT_eq/NVT_prod/NVT_vis/tcaf_all.xvg
+
+NREP_low=$((NREP_low+NREPS))
+NREP_high=$((NREP_high+NREPS))
+
+echo iRep = "$iRep"
+echo NREP_low = "$NREP_low"
+echo NREP_high = "$NREP_high"
+
+done # for iRep
+
+cd "$output_path" || error_report "Unable to change to $output_path directory" "$j" "$iMCMC" "post processing" 
+echo "In $PWD"
+
+###GreenKubo_analyze for all MCMC parameter sets
+python "$scripts_path"/GreenKubo_analyze.py --ilow 0 --ihigh $((NREP_low-1)) --nReps 1 --irho "$j" --sat
+
+done  # For each j
+
+cd "$output_path" || error_report "Unable to change to $output_path directory" "$j" "$iMCMC" "post processing" 
+###Create plots to compare with experimental data and correlations
+if [ "$Conditions_type" = "Saturation" ]
+then
+python "$scripts_path"/compare_TDE_REFPROP.py --comp "$Compound" --nrhomax $((j+1)) --sat
+else
+python "$scripts_path"/compare_TDE_REFPROP.py --comp "$Compound" --nrhomax $((j+1)) --"$Conditions_type"
+fi
+
+exit 0
+
+#######
+
diff --git a/Scripts/force_field_params b/Scripts/force_field_params
index aa2eae0..53e50eb 100644
--- a/Scripts/force_field_params
+++ b/Scripts/force_field_params
@@ -133,10 +133,10 @@ then
 
 cp "$input_path"/"$Compound"_temp_tors.top "$Compound".top 
 
-CH2_CH2_tors_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print}' < ~/MCMC_parameter_sets/MCMC_CH2_CH2_tors)
-CH2_CH_tors_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print}' < ~/MCMC_parameter_sets/MCMC_CH2_CH_tors)
-CH2_C_tors_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print}' < ~/MCMC_parameter_sets/MCMC_CH2_C_tors)
-CH_CH_tors_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print}' < ~/MCMC_parameter_sets/MCMC_CH_CH_tors)
+CH2_CH2_tors_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print}' < "$scripts_path"/../MCMC_parameter_sets/MCMC_CH2_CH2_tors)
+CH2_CH_tors_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print}' < "$scripts_path"/../MCMC_parameter_sets/MCMC_CH2_CH_tors)
+CH2_C_tors_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print}' < "$scripts_path"/../MCMC_parameter_sets/MCMC_CH2_C_tors)
+CH_CH_tors_sim=$(awk -v i="$((iMCMC+1))" 'FNR == i {print}' < "$scripts_path"/../MCMC_parameter_sets/MCMC_CH_CH_tors)
 
 sed -i -e s/some_CH2_CH2_tors/"${CH2_CH2_tors_sim[@]}"/ "$Compound".top
 sed -i -e s/some_CH2_CH_tors/"${CH2_CH_tors_sim[@]}"/ "$Compound".top
diff --git a/T293highP_Conditions/224TMHexane_liquid_box_N200 b/T293highP_Conditions/224TMHexane_liquid_box_N200
index e89ad20..9e9f505 100644
--- a/T293highP_Conditions/224TMHexane_liquid_box_N200
+++ b/T293highP_Conditions/224TMHexane_liquid_box_N200
@@ -2,13 +2,13 @@
 3.870464741
 3.845352056
 3.807294116
-3.77691126
+3.777484973
 3.734130802
 3.688040612
 3.664181974
 3.643648942
 3.626695498
 3.612599377
-3.60063831
-3.588669306
+3.598175125
+3.586016564
 Endline
\ No newline at end of file