Re: water equilibration

From: Narasimhan LOGANATHAN (Narasimhan.Loganathan_at_etu.univ-provence.fr)
Date: Mon Jun 06 2011 - 08:55:39 CDT

Hi,

Yes. I copied all the error message. It didnt provide any other information on the line which i went wrong.

Sincerely
Naresh
> ----------------------------------------
> From: Wang Yi <dexterwy_at_gmail.com>
> Sent: Mon Jun 06 15:42:26 CEST 2011
> To: Narasimhan LOGANATHAN <Narasimhan.Loganathan_at_etu.univ-provence.fr>
> Subject: Re: namd-l: water equilibration
>
>
> Hey Naresh,
>
> Did you copy-and-paste all the error message? Usually in addition to "FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE". NAMD should also tell you the line at which the execution went into error. Do you have that?
> ___________________________
>
> Yi (Yves) Wang
> Duke University
>
>
>
>
>
> ? 2011-6-6???9:07? Narasimhan LOGANATHAN ???
>
> > Hi all,
> > I am a newbie to NAMD. Right now i am trying to equilibrate water box.
> > I am not using the CHARMM forcefield. Hence i defined my own parameter file.
> > However when i tried to equilibrate or minimize the water i am getting the error
> >
> > ------------- Processor 0 Exiting: Called CmiAbort ------------
> > Reason: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
> >
> > Charm++ fatal error:
> > FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
> >
> >
> >
> > Herewith, i have attached the config file. Could someone let me know how can i proceed.
> >
> > structure water.psf
> > coordinates water.pdb
> >
> > set temperature 300 ;# Tcl variable
> > set outputname water-equi ;# Tcl variable
> >
> >
> > temperature $temperature ;# intialize velocities randomly using Boltzmann Distribution
> >
> > firsttimestep 0
> >
> > ## Input and ForceField Parameters ##
> > paratypeCharmm off
> > parameters clayff-namd.inp
> >
> > if {0} {
> > cellBasisVector1 31.212 0.0 0.0
> > cellBasisVector2 0.0 27.000 0.0
> > cellBasisVector3 0.0 0.0 30.000
> > cellOrigin 0.0 0.0 0.0
> > }
> >
> >
> > ##exclude scaled1-4 ##
> > ##1-4scaling 1.0 ##
> > cutoff 12.0
> > ##switching off ##
> > ## swtichdist 10.0 ## to be used when switching is on ##
> > pairlistdist 14.0 ;# cutoff + 2 in general
> > wrapAll on
> >
> > ## Integrator Parameters ##
> >
> > stepspercycle 2 ;# redefine pairlists every this many timesteps
> > timestep 1.0 ;# 1 fs/step
> > rigidBonds all ;# to keep the water molecules rigid
> > nonbondedFreq 1 ;# no. of timesteps used to calculate nonbonded interactions
> > fullElectFrequency 1 ;# no. of timesteps used to calculate electrostatic interactions
> >
> > ## Constant Temperature Control ##
> > langevin on ;# Uses langevin dynamics for controlling T (or) P
> > langevinDamping 1.0 ;# Damping Coefficient in pico seconds
> > langevinTemp $temperature ;# random noise at this level
> > langevinHydrogen no ;# no coupling of hydrogens
> >
> > ## Constant Pressure Control is done by the use of the langevin dynamics (see manual) ##
> >
> >
> > ## Particle Mesh Ewald ##
> > PME yes
> > PMEGridSpacing 1.0 ;# Alternatively we can specify the PMEgrid Manually in case direction ##
> >
> > #################################################################
> > ### Output Options ###
> > #################################################################
> >
> > outputname $outputname
> > restartfreq 500
> > dcdFreq 500
> > xstFreq 200
> > outputEnergies 100
> > outputPressure 100
> >
> >
> > ###################################################################
> > ### IMD Settings ###
> > ###################################################################
> >
> > if{0} {
> > IMDon on
> > IMDport 3000 ;# Enter this port number in VMD ##
> > IMDfreq 1 ;# send every 1 frame ##
> > IMDwait no ;# wait for VMD to connect before running ##
> > }
> >
> >
> > ###################################################################
> > ### Execution Script ###
> > ###################################################################
> > ## Minimization ##
> > if {0} {
> > minimize 100
> > reinitvels $temperature
> > }
> >
> > run 100000
> >
> > Thanks in advance
> > Naresh
> >
> >
>

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