[gmx-users] Use of Restraint itps

[Justin Lemkul]

On Wed, May 22, 2019 at 9:53 PM paul buscemi <pbuscemi at q.com> wrote:

> Justin,
>
> Thank you very much for the response.
>
> Obviously  grompp will apply the restraint to the argument of -r
> molecule.gro  and the  restraint.itp location is  in the top file  #include
> statement.  ( my (ITP directory ).    but how does grompp make the
> association between the -r argument and the itp ?    It would be more clear
> to me if the -r argument was the restraint.itp file itself.  Where the (
> missing ) link ?
>

The .itp specifies which atoms are restrained and how strongly. The
coordinates passed to -r are the origin of the biasing potential, I.e. “if
the atoms are here, the restraint force is zero.”

The coordinates and topology thus serve distinct but complementary
functions.

-Justin


> Paul
>
> > On May 22, 2019, at 12:14 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >
> >
> > On 5/22/19 10:41 AM, p buscemi wrote:
> >> Dear Users,
> >> In using restrain files, I place the restraint itp in a separated
> directory in which there may be other restraint files.
> >> I notice that within the restraint itp there is no specific reference
> to the molecule used to create the itp. I've run into an instance in which
> other than the intended itp was targeted by the molecule specified in the
> grompp statement.
> >>
> >> Is this as expected. ? Is there a mechanism to make the restraint itp
> specific for the called-out molecule ?
> >> Or - not completely out of the question - am I missing something ?
> >
> > grompp is doing what you tell it. You specify which file to #include and
> as long as grompp finds atom indices that are in range (e.g. start from 1
> and do not exceed the number of atoms in the relevant [moleculetype]), then
> it will happily do exactly what you're telling it to do.
> >
> > If you're going to accumulate a lot of files in one place, you need to
> be judicious in your file naming and what hacks you make to your .top file.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Office: 301 Fralin Hall
> > Lab: 303 Engel Hall
> >
> > Virginia Tech Department of Biochemistry
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.thelemkullab.com
> >
> > ==================================================
> >
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-- 

==========================================

Justin A. Lemkul, Ph.D.

Assistant Professor

Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com


==========================================