[gmx-users] Use of Restraint itps
pbuscemi at q.com
Thu May 23 03:53:03 CEST 2019
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 ?
> 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 A. Lemkul, Ph.D.
> Assistant Professor
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