Re: Using RMSD in colvar

From: Giacomo Fiorin (giacomo.fiorin_at_temple.edu)
Date: Tue May 04 2010 - 16:41:37 CDT

Hello Stefan, thanks for the offer. A "general" colvar tutorial is missing,
but keep in mind that the ABF tutorial, while covering the specific subject
of an ABF free energy calculation, already contains much of the information
you're looking for.

Did you check the 2.7b1 Users Guide or the 2.7b2 Users Guide? The latter
contains a specific example, which tells you that the "rmsd" block should be
either:

   rmsd {
      atoms { atomNumbers 1 2 3 }
      refPositionsFile ....
   }

or

   rmsd {
     atoms {
       # add all the C-alphas within residues 1 to 76 of segment "U"
        psfSegID U
       atomNameResidueRange CA 1-76
     }
     refPositionsFile ubq_ws.pdb
   }

In what you read, "myatoms" was just an example name for a group that's
named "group1", "group2", "atoms", "main", "ref", etc... depending on the
colvar component you choose ("distance", "dihedral", "rmsd", ...).

Giacomo

---- ----
Giacomo Fiorin
  ICMS - Institute for Computational Molecular Science
    Temple University
    1900 N 12 th Street, Philadelphia, PA 19122
mail: giacomo.fiorin_at_gmail.com
---- ----

On Mon, May 3, 2010 at 6:42 PM, Stefan Franzen <Stefan_Franzen_at_ncsu.edu>wrote:

>
>
>
> I have tried to apply the directions provided in the User Guide to use
> colvar. I am using the ubiquitin tutorial as a starting point. In fact,
> you might say I am developing a tutorial section for colvar, which I would
> be happy to make available (once I figure it out). I am quite frustrated
> trying to apply the instructions. the "distance" works fine. But, the next
> step for me of RSMD does not work no matter what I do. Here are two things
> that I have tried. I have included my working file, which just tracks the
> distance between the ends of ubiquitin as an example.
>
> # option 1: put in the atom numbers #
>
> colvar {
> rmsd {
> atoms { 1 2 3 }
> refPositionsFile ubq_ws.pdb
> }
> }
>
> # option 2: put in the C-alphas #
>
> myatoms {
> # add all the C-alphas within residues 1 to 76 of segment "U"
> psfSegID U
> atomNameResidueRange CA 1-76
> }
>
> colvar {
> rmsd {
> atoms { myatoms }
> refPositionsFile ubq_ws.pdb
> }
> }
>
> Thank you,
> Stefan
>
> --
> Stefan Franzen
> Professor of Chemistry
> North Carolina State University
> Raleigh, NC 27695
> Phone: 919-515-8915
>
>
>
> --
> Stefan Franzen
> Professor of Chemistry
> North Carolina State University
> Raleigh, NC 27695
> Phone: 919-515-8915
>

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