Re: the fep error in third part of config file

From: Brian Radak (brian.radak_at_gmail.com)
Date: Mon Oct 15 2018 - 14:17:23 CDT

It would really help if you posted the exact error message.

Based on your input alone, it would appear that you have used invalid
keywords. "lambda" and "lambda2" should probably be "alchLambda" and
"alchLambda2". I don't know what you mean by "dlambda" as there is no such
keyword in the manual.

I also suspect that your for-loop will fail since alchLambda and
alchLambda2 must both be between 0 and 1.

HTH,
BKR

On Mon, Oct 15, 2018 at 10:51 AM soroush ziaei <soroush.ziaei7337_at_gmail.com>
wrote:

> 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
>
> }
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>

This archive was generated by hypermail 2.1.6 : Sat Dec 07 2019 - 23:20:11 CST