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xmdff_template.namd
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############################################################################
#cr
#cr (C) Copyright 1995-2009 The Board of Trustees of the
#cr University of Illinois
#cr All Rights Reserved
#cr
############################################################################
############################################################################
# RCS INFORMATION:
#
# $RCSfile: xmdff_template.namd,v $
# $Author: ryanmcgreevy $ $Locker: $ $State: Exp $
# $Revision: 1.8 $ $Date: 2017/04/25 15:55:31 $
#
############################################################################
#
# DESCRIPTION:
#
# NAMD template file for MDFF simulations.
#
# Authors: Leonardo Trabuco <[email protected]>
# Elizabeth Villa <[email protected]>
# Kwok-Yan Chan <[email protected]>
#
############################################################################
firsttimestep 0
# Force-Field Parameters
exclude scaled1-4
1-4scaling $SCALING_1_4
switching on
dielectric $DIEL
margin $MARGIN
if {$GBISON} {
gbis on
alphacutoff 14.
switchdist 15.
cutoff 16.
pairlistdist 17.
ionconcentration 0.1
solventDielectric 80.0
sasa on
} else {
cutoff 10.
switchdist 9.
pairlistdist 11.
}
# Integrator Parameters
timestep 1.0 ;# 1fs/step
rigidBonds water ;# TIP3P
nonbondedFreq 2
fullElectFrequency 4
stepspercycle 20
# Constant Temperature Control
if {$ITEMP == $FTEMP} {
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $FTEMP
langevinHydrogen off ;# don't couple langevin bath to hydrogens
} else {
reassignFreq 1000
if {$FTEMP > $ITEMP} {
reassignIncr 10
} else {
reassignIncr -10
}
reassignTemp $ITEMP
reassignHold $FTEMP
}
# Output
outputName $OUTPUTNAME
restartfreq 1000
dcdfreq 1000
outputEnergies 100
outputPressure 100
# gridForces (to apply forces from 3D potential)
if {$GRIDON} {
mgridForce on
for {set i 0} {$i < [llength $GRIDFILE]} {incr i} {
mgridForceFile $i [lindex $GRIDPDB $i]
mgridForceCol $i O
mgridForceChargeCol $i B
mgridForcePotFile $i [lindex $GRIDFILE $i]
mgridForceScale $i [lindex $GSCALE $i] [lindex $GSCALE $i] [lindex $GSCALE $i]
}
}
# extraBonds (for secondary structure restraints)
if {$EXTRAB != 0} {
extraBonds yes
foreach fil $EXTRAB {
extraBondsFile $fil
}
}
# Positional restraints
if {$CONSPDB != 0} {
Constraints yes
ConsExp 2
ConsRef $CONSPDB
ConsKFile $CONSPDB
ConskCol $CONSCOL
}
# Fixed atoms
if {$FIXPDB != 0} {
fixedAtoms yes
fixedAtomsFile $FIXPDB
fixedAtomsCol $FIXCOL
}
#BEGIN XMDFF NECESSARY FUNCTIONS
if {[info exists INPUTNAME]} {
set env(VMDARG) [list $PSFFILE $INPUTNAME $GRIDFILE $REFS $BFS $MASK $CRYSTPDB $MASKRES $MASKCUTOFF $XMDFFSEL $AVERAGE]
exec -ignorestderr vmd -dispdev text -e xmdff_phenix.tcl > map.log
} else {
set env(VMDARG) [list $PSFFILE $PDBFILE $GRIDFILE $REFS $BFS $MASK $CRYSTPDB $MASKRES $MASKCUTOFF $XMDFFSEL $AVERAGE]
exec -ignorestderr vmd -dispdev text -e xmdff_phenix.tcl > map.log
}
if {$MS != 0} {
minimize $MS
reinitvels $ITEMP
}
if {$ITEMP != $FTEMP} {
set ANNEALSTEP [expr abs($FTEMP-$ITEMP)*100]
run $ANNEALSTEP
set env(VMDARG) [list $PSFFILE $OUTPUTNAME $GRIDFILE $REFS $BFS $MASK $CRYSTPDB $MASKRES $MASKCUTOFF $XMDFFSEL $AVERAGE]
exec -ignorestderr vmd -dispdev text -e xmdff_phenix.tcl > map.log
for {set i 0} {$i < [llength $REFS]} {incr i} {
set grid [expr [llength $GRIDFILE]-[llength $REFS]+$i]
reloadGridforceGrid $grid
}
}
for {set i 0} {$i < $TS/$REFINESTEP} {incr i} {
run $REFINESTEP
set env(VMDARG) [list $PSFFILE $OUTPUTNAME $GRIDFILE $REFS $BFS $MASK $CRYSTPDB $MASKRES $MASKCUTOFF $XMDFFSEL $AVERAGE]
exec -ignorestderr vmd -dispdev text -e xmdff_phenix.tcl > map.log
for {set j 0} {$j < [llength $REFS]} {incr j} {
set grid [expr [llength $GRIDFILE]-[llength $REFS]+$j]
reloadGridforceGrid $grid
}
}