[gmx-users] Use of Restraint itps

[paul buscemi]

Justin,  Certainly appreciate the help on this basic issue.

getting closer….  I understand your response.  

Now, to clarify — how does the mdp ( or grompp )  know which itp file among the #include’s  is to be used as the restraint file.  Is that identified with the define = statement in the mdp ? so if my restraint is MOL.posres.itp , I would state “define  = DMOL.posres.itp “ ?

Paul

> On May 22, 2019, at 9:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 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
> 
> 
> ==========================================
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