Re: collective variable calculation from dcd file

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Thu Dec 22 2011 - 05:20:15 CST

Hi Giovanni,

I think your problem here is multiple time-step, which does not make
much sense when reading frames from a DCD file. I have seen NAMD react
badly to this and segfault.

Try setting fullElectFrequency to 1.

Best,
Jerome

On 21 December 2011 21:44, Giovanni Bellesia
<giovanni.bellesia_at_gmail.com> wrote:
> Hi all,
>
> I'm wondering if it's possible to calculate  a collective variable (i.e., a
> dihedral calculated over 4 groups of atoms)
> from a dcd trajectory file.
> I am pasting the configuration file I am trying to use.
> What it does is ... it computes the state of the variable at the first step
> and then it stops with error message "Segmentation default"
>
> Thanks,
>
> Giovanni
>
> --------------
>
> structure       ./structure.psf
> coordinates     ./coords.pdb
>
> set temperature    310
> set outputname     out1
>
> firsttimestep      0
>
>
> # Input
> paraTypeCharmm      on
> vdwGeometricSigma yes
> parameters          ./opls.prm
> temperature         $temperature
>
> # Force-Field Parameters
> exclude             scaled1-4
> 1-4scaling           1.0
>
> # Constant Temperature Control
> langevin             on
> langevinDamping      1.0
> langevinTemp         $temperature
> langevinHydrogen     no
>
> # GBIS parameters
> GBIS on
> ionConcentration 0.3
> alphaCutoff 12
>
> # Nonbonded parameters
> switching on
> switchdist 12
> cutoff 13
> pairlistdist 14.5
>
> # Multistep parameters
> timestep            2.0
> rigidBonds          all
> nonbondedFreq       1
> fullElectFrequency  2
> stepspercycle       10
>
> colvars              on
> colvarsConfig        Dihedral.in
>
> outputName          $outputname
> binaryOutput    no
>
> set ts 1
>
> coorfile open dcd test1.dcd
>
> # Read all frames until nonzero is returned.
> while { ![coorfile read] } {.
>   firstTimestep $ts
>   run 0
>   incr ts 1
> }
> coorfile close

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