Re: Multiple Harmonic Constraints

Date: Wed Jun 15 2005 - 08:37:34 CDT

(Sorry if I missed an earlier reply to this post...)

Sascha, I do believe your issue is simple to solve. In fact, you have
complete freedom to specify the strength of the restraint force for each
atom in your system individually. The numbers that you put into your chosen
column in the "consref" file provide an atom-by-atom specification of the
force constant to be used. So if you want certain atoms to be restrained
more strongly, you just put bigger numbers in the appropriate column for
those atoms; if you want no restraint on certain atoms, you put a zero in
the corresponding column.

For a large system, you would probably want to use a VMD script (if you're
familiar with that program) to easily create your "consref" file, with
certain numbers in the "conskcol" column for certain atom types.

Hope this was helpful!

- Erik

C. Erik Nordgren, Ph.D.
Department of Chemistry
University of Pennsylvania

Quoting Sascha Tayefeh <>:

> Hi!
> Maybe I need to add an example to my previouse request to make things
> clearer. What I want to do is something like this:
> All Protein-Backbone harmonically const. with factor 10x
> All Protein-Non-Backbone harmonically const. with factor 5x
> Some further harmonically constr. with factor 2x
> I know how to create my PDBs and how to make the section. I also know
> how to apply *one* of those constr. mentioned above, eg:
> --------
> constraints on
> consexp 10
> conskfile ./data/sys7_rest_1b.pdb
> consref ./data/sys7_rest_1b.pdb
> conskcol B
> selectConstraints on
> selectConstrX off
> selectConstrY off
> selectConstrZ on
> ---------
> What I don't know is how to add *all* of those constr. *simultanuously*.
> P.S. I didn't quite get the idea on how to respond to an e-mail in a
> mailing-list, so I just added a postfix "Re: " to the subject. If this
> does not follow up the original message, I would very appreciate any
> suggestions...
> Thanks again!
> --
> Sascha Tayefeh <>
> Dipl.-Biol, PhD-Student
> ---
> Darmstadt University of Technology
> Physical Chemistry I

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