Re: collective variable calculation from dcd file

From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Wed Dec 21 2011 - 15:15:06 CST

Giovanni,

If you want to obtain numerical values of your dihedrals only, you could
do this by analyzing dcd in VMD or Vega. But if you want energies
associated with those dihedrals, during simulation some procedure for
'mapping' of the free energy should be applied. If you define such
forces during simulation (not mentioned in your mail), you should find
corresponding output files in simulation output. Along with this, there
is some doubtful values in your basic configuration, more data about
your system will be useful to help members of the mailing list to give
you useful suggestions.

Branko

On 12/21/2011 9:44 PM, Giovanni Bellesia 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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