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msld_flat.inp
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msld_flat.inp
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* CHARMM input file for Multi-Site lambda-dynamics
* MSLD references:
* J.L. Knight and C.L. Brooks III. Multi-site lambda-dynamics:
* free energy method for simulating Structure-Activity Relationship
* studies. J. Chem. Theory Comput. 7, 2728-2739 (2011).
* J.L. Knight and C.L. Brooks III. Applying efficient
* implicit non-geometric constraints in free energy simulations.
* J. Comput. Chem. 32, 3423-3432 (2011).
* Stream file for MSLD created by process.py
* Written by Ryan Hayes 2016-06-18
*
if ?blade .ne. 1 then
echo "Test NOT performed. Blade must be defined in pref.dat"
stop
endif
set fnex = 5.5
set temp = 298.15
stream "variables@{IFLAT}.inp"
bomblev -1
stream "prep/@{SYSNAME}.inp"
! Set nonbonded options
stream ../nbond.str
faster on
! system "mkdir -p res dcd"
if @{IFLAT} .eq. 1 then
cons harm abso force 10.0 mass select (segid PROT .or. segid LIG .or. segid MOL) show end comp
mini sd nstep 200 nprint 10 step 0.005
cons harm clear
! release restraints and minimize everything
mini sd nstep 250 nprint 10 step 0.005 !! Do min, Steepest-Decent
write psf card name ../prep/minimized.psf
* after minimization psf
*
write coor card name ../prep/minimized.crd
* after minimization crd
*
write coor pdb form name ../prep/minimized.pdb
* after minimization pdb
*
bomblev 0
else
read coor card name prep/minimized.crd
endif
!---------------------------------------------------------------------------
! Setup of dynamics run
!---------------------------------------------------------------------------
if @nreps .eq. 1 then
set myrep = 0
else
!! Initiate BP-REX MSLD
set dph = 0.5
calc sph = 7.0 - @dph*@ncentral
repd fast nrep @nreps EXLM FREQuency 1000 MSPH SPH @sph DPH @dph unit 27
!! Direct output of replicas to their individual files
set myrep = ?myrep
endif
open write form unit 28 name output_@myrep
outu 28
stream "../nbshift/vb.inp"
shake fast bonh param
scalar fbeta set 0.1 sele all end
domdec gpu only dlb off ndir 1 @nnodes 1
!! Heating run of 100 ps
open unit 21 write unform name "dcd/@{SYSNAME}_heat.dcd_@MYREP"
open unit 22 write form name "res/@{SYSNAME}_heat.res_@MYREP"
open unit 24 write file name "res/@{SYSNAME}_heat.lmd_@MYREP"
if nreps .gt. 1 then
open write form unit 27 name "@{SYSNAME}_heat.rex_@MYREP"
endif
if @?restartfile eq 0 then
set resttoken = start
set iurest = -1
else
set resttoken = restart
open unit 23 read form name ../@{RESTARTFILE}_@MYREP
set iurest = 23
endif
calc seed = @seed
calc pmass = ?natom * 0.12
dynamics cpt @resttoken -
blade prmc iprs 100 pref 1 prdv 100 -
iseed @seed @seed @seed @seed -
timestep 0.002 - !!timestep interval
nstep @esteps - !!no. of steps (== 200 ps)
nprint 1000 - !!freq of printout
iprfrq 1000 - !!freq of calc avg/rms energy
nsavc 1000 - !!freq of writing coordinates
nsavl 10 - !!freq of writing lambda histograms
isvfrq @esteps - ! 10000 - !!freq of writing out restart files
iunread @iurest - !!read restart file
iuncrd 21 - !!write out coordinates
iunwri 22 - !!write out restart file
iunldm 24 - !!write out lambda histograms and biasing potential
firstt @temp - !!initial temp
finalt @temp - !!final temp
tstruc @temp - !!temp at which starting structure has been equilibrated
tbath @temp - !!temp of langevin bath
pconstant - !! use constant pressure (pressure.doc recommendations)
pmass @pmass - !! pressure "mass" 2% of mass or 400.0 amu
pref 1.0 - !! pressure in atm
pgamma 20.0 - !! pressure collision frequency
hoover -
reft @temp -
tmass 1000 -
ichecw 0 - !!do not scale velocities to final temp (i.e. equilibrate)
ihtfrq 0 - !!freq of heating
ieqfrq 0 - !!freq of scaling/assigning velocity(X)
iasors 1 - !!assign velocities during heating (0 will be scale velocities)
iasvel 1 - !!using gaussian distribution to assign velocities
iscvel 0 -
inbfrq -1 -
ilbfrq 0 -
imgfrq -1 -
ntrfrq 0 - ! 500 -
echeck -1 !!energy tolerance check before crashing
!! Production run of 100 ps / 1 ns
open unit 21 write unform name "dcd/@{SYSNAME}_flat.dcd_@MYREP"
open unit 22 write form name "res/@{SYSNAME}_flat.res_@MYREP"
! open unit 23 read form name "res/@{SYSNAME}_heat.res_@MYREP"
open unit 24 write file name "res/@{SYSNAME}_flat.lmd_@MYREP"
if nreps .gt. 1 then
open write form unit 27 name "@{SYSNAME}_flat.rex_@MYREP"
endif
calc pmass = ?natom * 0.12
dynamics cpt start -
blade prmc iprs 100 pref 1 prdv 100 -
timestep 0.002 - !!timestep interval
nstep @nsteps - !!no. of steps (== 2 ns)
nprint 1000 - !!freq of printout
iprfrq 1000 - !!freq of calc avg/rms energy
nsavc 1000 - !!freq of writing coordinates
nsavl 10 - !!freq of writing lambda histograms
isvfrq @nsteps - ! 10000 - !!freq of writing out restart files
iunread -1 - ! 23 - !!read restart file
iuncrd 21 - !!write out coordinates
iunwri 22 - !!write out restart file
iunldm 24 - !!write out lambda histograms and biasing potential
firstt @temp - !!initial temp
finalt @temp - !!final temp
tstruc @temp - !!temp at which starting structure has been equilibrated
tbath @temp - !!temp of langevin bath
pconstant - !! use constant pressure (pressure.doc recommendations)
pmass @pmass - !! pressure "mass" 2% of mass or 400.0 amu
pref 1.0 - !! pressure in atm
pgamma 20.0 - !! pressure collision frequency
hoover -
reft @temp -
tmass 1000 -
ichecw 0 - !!do not scale velocities to final temp (i.e. equilibrate)
ihtfrq 0 - !!freq of heating
ieqfrq 0 - !!freq of scaling/assigning velocity(X)
iasors 1 - !!assign velocities during heating (0 will be scale velocities)
iasvel 1 - !!using gaussian distribution to assign velocities
iscvel 0 -
inbfrq -1 -
ilbfrq 0 -
imgfrq -1 -
ntrfrq 0 - ! 500 -
echeck -1 !!energy tolerance check before crashing
!----------------------------------------------------------------------------
! Write out structure after simulation
!----------------------------------------------------------------------------
NOE
RESET
END
cons harm clear
!write psf card form name "@{SYSNAME}_flat.psf_@MYREP"
!* after dynamics psf
!*
write coor pdb form name "@{SYSNAME}_flat.pdb_@MYREP"
* after dynamics pdb
*
!---------------------------------------------------------------------------
! Analyze l-dynamics output
!---------------------------------------------------------------------------
open unit 44 read file name "res/@{SYSNAME}_flat.lmd_@MYREP"
traj lamb print ctlo 0.95 cthi 0.99 first 44 nunit 1
stop