[gmx-users] Re: Analysis tools and triclinic boxes

[Justin Lemkul]

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 <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Analysis tools and triclinic boxes
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <5277E854.9000305 at 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

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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