From: johan strumpfer (johan.ks.uiuc_at_gmail.com)
Date: Tue Jun 07 2011 - 09:44:33 CDT
Hi Naresh,
As Bjoern said, your input script looks okay so to better diagnose it
we need more information. Could you rule out that it is not an error
with the custom force-field file and also post the contents of the log
file to give us more information.
Cheers,
Johan
----------------------------------------------------------------
Johan Strumpfer (johanstr_at_ks.uiuc.edu)
Theoretical and Computational Biophysics Group
3115 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801, USA
On Tue, Jun 7, 2011 at 10:03 AM, Narasimhan LOGANATHAN
<Narasimhan.Loganathan_at_etu.univ-provence.fr> wrote:
> 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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