On 11/5/13 7:14 PM, Stephanie Teich-McGoldrick wrote:
Message: 5
Date: Mon, 04 Nov 2013 13:32:52 -0500
From: Justin Lemkul <jalem...@vt.edu>
Subject: Re: [gmx-users] Analysis tools and triclinic boxes
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <5277e854.9000...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Justin,
Thanks for the response. My question was prompted by line 243 in
gmx_cluster.c which states "/* Should use pbc_dx when analysing multiple
molecueles,but the box is not stored for every frame.*/" I just wanted to
verify that analysis tools are written for any box shape.
I have never had any problems with any of the analysis tools using any of the
box shapes, though that of course does not negate the possibility of problems.
The comments in pbc.h describe all of the functions quite well and what the
potential issues might be. If there is a demonstrable problem with something,
that is certainly worth pursuing.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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