Re: water equilibration

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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