Re: collective variable calculation from dcd file

From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Wed Dec 21 2011 - 15:38:39 CST

OK,

Try then with VegaZZ (free, http://www.ddl.unimi.it/), you can define
very complicated structural queries in it, and analyze those queries in
fast manner. For your dihedrals maybe angles between two plain can solve
the problem.

Branko

On 12/21/2011 10:20 PM, Giovanni Bellesia wrote:
> 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
> <mailto: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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>
>
>
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