Re: error in (runfepmin)

From: HEMANTH H 18310019 (hemanth.h_at_iitgn.ac.in)
Date: Sun Oct 21 2018 - 23:13:26 CDT

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>
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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