From: Giovanni Bellesia (giovanni.bellesia_at_gmail.com)
Date: Wed Dec 21 2011 - 15:20:27 CST
VMD has the "measure dihed" command which (I think) cannot be used in my
case as it requires 4 atom indexes.
I basically have 4 COMs from 4 different groups of atoms.
I have a simple TCL script which is calculating the dihedral angle defined
by 4 COMs, but (as you can imagine) it's very slow.
I was just looking for an alternative solution.
Giovanni
On Wed, Dec 21, 2011 at 2:15 PM, Branko <bdrakuli_at_chem.bg.ac.rs> wrote:
> **
> 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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