Re: Using RMSD in colvar

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Tue May 04 2010 - 15:07:38 CDT

Hi Stefan,

Your message reminds us that users need examples of working inputs for
the colvars module. The new version of the ABF tutorial should
hopefully help a little.
In your input, there is a problem with the way the atom group is
defined. One correct syntax would be:

colvar {
   rmsd {
      atoms {
           atomNumbers { 1 2 3 }
      }
      refPositionsFile ubq_ws.pdb
   }
}

and your other version should read:

colvar {
   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
   }
}

One important remark: in principle, wrong input should result in
informative error messages. If the messages you got were not helpful,
we will try and improve them.

Best,
Jerome

On 4 May 2010 00:42, 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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