Re: restraining groups of atoms

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Mon Jun 20 2011 - 07:56:06 CDT

Hi Massimiliano,

This can be done with a "colvar" restraint (see Collective
Variable-based Calculations in the user's guide). The colvar
configuration file would be a plain text file containing something
like this:

colvarsTrajFrequency 100 # output values every 100 steps

colvar {
  name d # needed to identify the variable

  distance {
    group1 {
      atomNumbers 1 2 3
    }
    group2 {
      atomNumbers 4 5 6
    }
  }
}

harmonic {
  colvars d
  centers 3.0
  forceConstant 5.0
}

Best,
Jerome

On 20 June 2011 14:03, Massimiliano Porrini <M.Porrini_at_ed.ac.uk> wrote:
> Dear namd-lers,
>
> I am running some MD trajectories of a dimer in implicit solvent.
>
> What I would like to do is to put a harmonic potential between
> the centers of mass of each monomer in order to prevent them to
> go too far away one from another.
>
> Is that possible with NAMD ?
>
> What I found in the manual is only about harmonic restraining of
> atoms, bonds, angles and dihedrals.
>
> Many thanks in advance for your help.
>
> All the best,
> MP
>
>
> --
> Dr Massimiliano Porrini
> Institute for Condensed Matter and Complex Systems
> School of Physics & Astronomy
> The University of Edinburgh
> James Clerk Maxwell Building
> The King's Buildings
> Mayfield Road
> Edinburgh EH9 3JZ
>
> Tel +44-(0)131-650-5229
>
> E-mails : M.Porrini_at_ed.ac.uk
>              mozz76_at_gmail.com
>              maxp_at_iesl.forth.gr
>
>

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