[gmx-users] Flat-bottomed potential from user-defined reference

[Justin Lemkul]

On 11/3/15 5:24 AM, Cosseddu, S.M. wrote:
> Dear all,
>
> I am trying to apply a spherical flat-bottomed potential to maintain some molecules within a certain region. By default, GROMACS uses the initial coordinates as reference. Is there any way to provide different references?
>

Not quite right.  GROMACS uses the initial coordinates (grompp -c) if there are 
no additional restraint coordinates (grompp -r) provided.  So you can easily 
pass a coordinate file to the -r argument that specifies whatever coordinates 
you like as a reference.  Using "non-physical" coordinates is fairly typical 
with a flat-bottom restraint.

-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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