From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Mon Oct 22 2018 - 13:51:10 CDT
To expand on this a bit further, whenever you see a "$", that is an indication to the tcl interpreter that you are talking about a variable name. You don't seem to have a variable "temp", which is set with "set temp 3.14159" if you wanted $temp to be replace with 3.14159 wherever it appears. Note that saying "temperature 0" does not set a variable, and is only read in by NAMD's configuration file parser.
-Josh
On 2018-10-21 22:19:04-06:00 owner-namd-l_at_ks.uiuc.edu wrote:
You have set the variable temperature to zero, while the last line reads $temp which refers to a different variable which is undefined. So either rename temperature to temp or change temp to temperature.
Best,
Hemanth H
On Mon 22 Oct, 2018, 4:34 AM soroush ziaei, <soroush.ziaei7337_at_gmail.com<mailto:soroush.ziaei7337_at_gmail.com>> wrote:
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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