From: soroush ziaei (soroush.ziaei7337_at_gmail.com)
Date: Mon Oct 15 2018 - 09:50:25 CDT
Hi all,
I want to calculate fep in namd but when I run this simulation, an fatal error appears in the terminal about configuration file. I puted some parameters here:
[Note: the first conf file is about minimization and the second one is related to increasing temperature and the last one that is loaded below]
I think the problem is about rand.fep (pdb) as input for fep, right?
i'll be happy, if someone help me.
Best regard, soroush
# NAMD config file
numsteps 15000000
structure solvate.psf
coordinates solvate.pdb
outputName eq2
XSTfile eq2.xst
bincoordinates eq1.coor
binvelocities eq1.vel
extendedSystem eq1.xsc
langevin on
langevinDamping 3
langevinTemp 310
langevinHydrogen on
useGroupPressure yes
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1
langevinPistonPeriod 100
langevinPistonDecay 50
langevinPistonTemp 310
fep on
fepfile rand.fep
fepCol B
fepOutFile rand.fepout
fepOutFreq 5
fepEquilSteps 3200
set step 0
set dstep 0.025
dlambda $dstep
while {$step < 1} {
firsttimestep 0
lambda $step
set step [expr $step+$dstep]
lambda2 $step
run 6400
}
switching on
switchDist 10
cutoff 12
pairlistdist 14
margin 3
binaryOutput yes
binaryRestart yes
parameters par file.par
parameters par2.prm
paraTypeCharmm on
wrapAll yes
wrapNearest yes
COMmotion no
outputEnergies 500
outputTiming 500
xstFreq 500
dcdFreq 250
restartFreq 500
timestep 1
nonBondedFreq 2
fullElectFrequency 4
stepsPerCycle 20
Pme on
PmeGridSizeX 40
PmeGridSizeY 40
PmeGridSizeZ 40
exclude scaled1-4
1-4scaling 1
if {1} {
fixedAtoms off
fixedAtomsFile fix.pdb
fixedAtomsCol B
fixedAtomsForces off
}
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