From: Narasimhan LOGANATHAN (Narasimhan.Loganathan_at_etu.univ-provence.fr)
Date: Tue Jun 07 2011 - 09:03:23 CDT
Hi,
Yes. The custom force-field file is in X-plor format only and still i have the
errors.
Sincerely,
Naresh
> ----------------------------------------
> From: johan strumpfer <johanstr_at_ks.uiuc.edu>
> Sent: Mon Jun 06 15:59:05 CEST 2011
> To: Narasimhan LOGANATHAN <Narasimhan.Loganathan_at_etu.univ-provence.fr>
> Subject: Re: namd-l: water equilibration
>
>
> Hi Naresh,
>
> You set paraTypeCharmm off, this would mean that your custom
> force-field is in Xplor format - is this the case?
>
> Cheers,
> Johan
>
> ------------------------------------------------------------------------------------------------------
> Johan Strumpfer: johanstr_at_ks.uiuc.edu www.ks.uiuc.edu/~johanstr
> Theoretical and Computational Biophysics Group
> 3115 Beckman Institute
> University of Illinois at Urbana-Champaign
> 405 N. Mathews
> Urbana, IL 61801, USA
> ------------------------------------------------------------------------------------------------------
>
>
>
> On Mon, Jun 6, 2011 at 9:55 AM, Narasimhan LOGANATHAN
> <Narasimhan.Loganathan_at_etu.univ-provence.fr> wrote:
> > 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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