From: johan strumpfer (johanstr_at_ks.uiuc.edu)
Date: Mon Jun 06 2011 - 08:59:05 CDT
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
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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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