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heat.conf
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heat.conf
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#############################################################
## JOB DESCRIPTION ##
# Heating
#############################################################
#Global parameters
set prot pr3_prod
set lig mol51
set box 67.491049
set iseed 185212
set step final-mini
# specify the parameter files location
paraTypeCharmm on
parameters toppar/par_all36_prot.prm
parameters toppar/par_all36_na.prm
parameters toppar/par_all36_carb.prm
parameters toppar/par_all36_lipid.prm
parameters toppar/par_all36_cgenff.prm
parameters toppar_water_ions_namd.str
parameters $lig.prm
#specify the location of the psf and pdb files
structure ../$prot-$lig-neutralized.psf
coordinates $step/$prot-$lig-finalmini_1.coor
extendedSystem $step/$prot-$lig-finalmini_1.xsc
# specify the temperature here
set temperature 298
set outputname heat/$prot-$lig-heat
# Periodic Boundary Conditions
cellBasisVector1 $box 0. 0.0
cellBasisVector2 0.0 $box 0.0
cellBasisVector3 0.0 0 $box
# These are specified by CHARMM
exclude scaled1-4 # non-bonded exclusion policy to use "none,1-2,1-3,1-4,or scaled1-4"
# 1-2: all atoms pairs that are bonded are going to be ignored
# 1-3: 3 consecutively bonded are excluded
# scaled1-4: include all the 1-3, and modified 1-4 interactions
# electrostatic scaled by 1-4scaling factor 1.0
# vdW special 1-4 parameters in charmm parameter file.
1-4scaling 1.0
switching on
vdwForceSwitching yes; # New option for force-based switching of vdW
# if both switching and vdwForceSwitching are on CHARMM force
# switching is used for vdW forces.
# You have some freedom choosing the cutoff
cutoff 12.0; # may use smaller, maybe 10., with PME
switchdist 10.0; # cutoff - 2.
# switchdist - where you start to switch
# cutoff - where you stop accounting for nonbond interactions.
# correspondence in charmm:
# (cutnb,ctofnb,ctonnb = pairlistdist,cutoff,switchdist)
pairlistdist 16.0; # stores the all the pairs with in the distance it should be larger
# than cutoff( + 2.)
stepspercycle 20; # 20 redo pairlists every ten steps
pairlistsPerCycle 2; # 2 is the default
# cycle represents the number of steps between atom reassignments
# this means every 20/2=10 steps the pairlist will be updated
#Bond Paramters
rigidBonds all; # Bound constraint all bonds involving H are fixed in length
nonbondedFreq 1; # nonbonded forces every step
fullElectFrequency 1; # PME every step
wrapWater on; # wrap water to central cell
wrapAll on; # wrap other molecules too
# PME (for full-system periodic electrostatics)
PME yes;
PMEInterpOrder 6; # interpolation order (spline order 6 in charmm)
PMEGridSpacing 1.0; # maximum PME grid space / used to calculate grid size
# Output
# all output files will have the same name but different extensions
# our outputname is final_min, so
# final_min.dcd final_min.coor etc files will be created
outputName $outputname
restartfreq 100;
dcdfreq 100;
dcdUnitCell yes;
binaryoutput no;
#############################################################
### EXECUTION SCRIPT ##
##############################################################
#
seed $iseed # Random number seed used to generate initial Maxwell distribution of velocities
numsteps 10000 # Number of integration steps
temperature 198 # Initial velocity distribution is performed to meet this Initial temperature (in K)
reassignFreq 100 # Number of steps between reassignment of velocities (e)
reassignIncr 1 # Increment used to adjust temperature during temperature reassignment
reassignHold $temperature # The value of temperature to be kept after heating is completed