[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

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 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

Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list