[gmx-users] Use of Restraint itps

Justin Lemkul jalemkul at vt.edu
Wed May 22 19:14:30 CEST 2019

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
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129


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