[gmx-users] Position restraining of ions.

[Justin Lemkul]

On 7/16/15 9:37 AM, anu chandra wrote:
> Thanks for the reply. I have one more quick query about position restrain
> here and its about restraining some pat of the whole protein.
>
> Say, I have a protein of 400 aminoacinds ( ie., residues no. 1-400). I
> would like to set up position restrain in such way that backbone atoms of
> residues 101-200 and 301-400 assign a fixed restrain force of 1000 KJ
> through-out the equilibration process and rest of the atoms ( ie, sidechain
> atoms of 101-200 and 301-400 and all atoms of residues 1-100 and 201-300)
> have descending order of restrain force starting with 1000 KJ, then 500 KJ,
> followed by 100 KJ, 50 KJ and finally, 0 KJ. How can I generate such a
> position restrain file in Gromcas?
>

It can't be done with a single restraint file, but you can conditionally trigger 
different force constants.  This is actually what CHARMM-GUI does to equilibrate 
the lipids, so look at the same logic.  Create multiple restraint .itp files 
with genrestr and suitable index groups.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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