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

Cosseddu, S.M. s.m.cosseddu at vu.nl
Tue Nov 3 15:16:54 CET 2015


Thank you Justin, 

This is exactly what I was looking for, and I somehow overlooked -r flag. 

Best regards
Salvatore

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Justin Lemkul [jalemkul at vt.edu]
Sent: 03 November 2015 12:11
To: gmx-users at gromacs.org
Subject: [Spam] Re: [gmx-users] Flat-bottomed potential from user-defined reference

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

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