Re: water equilibration

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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