From: soroush ziaei (soroush.ziaei7337_at_gmail.com)
Date: Sun Oct 21 2018 - 18:02:24 CDT
hi all,
at the first step of fep simulation this error message appears:
TCL: can't read "temp": no such variable
FATAL ERROR: can't read "temp": no such variable
while executing
"runFEPmin 0.0 0.0 0.0 $numSteps $numMinSteps $temp"
(file "0.namd" line 83)
what should i do? please help me.
& i provide one of the config file here:
# NAMD config file
numsteps 20000
structure solvate.psf
coordinates solvate.pdb
outputName eq0
XSTfile eq0.xst
minimization on
temperature 0
cellBasisVector1 36.0 0.0 0.0
cellBasisVector2 0.0 36.0 0.0
cellBasisVector3 0.0 0.0 36.0
cellOrigin -0.00766 0.02745 -0.01082
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 200
outputTiming 200
xstFreq 200
dcdFreq 100
restartFreq 200
timestep 1
nonBondedFreq 2
fullElectFrequency 4
stepsPerCycle 20
useGroupPressure yes
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1
langevinPistonPeriod 100
langevinPistonDecay 50
langevinPistonTemp 310
Pme on
PmeGridSizeX 40
PmeGridSizeY 40
PmeGridSizeZ 40
exclude scaled1-4
1-4scaling 1
# FEP PARAMETERS
source fep.tcl
alch on
alchType FEP
alchFile solvate.fep
alchCol B
alchOutFile aqua-equil.fepout
alchOutFreq 1000
alchVdwLambdaEnd 1.0
alchElecLambdaStart 0.5
alchVdWShiftCoeff 4.0
alchDecouple on
alchEquilSteps 10000
set numSteps 50000
set numMinSteps 100
runFEPmin 0.0 0.0 0.0 $numSteps $numMinSteps $temp
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