[gmx-users] histogram of distance between similar molecules

Srinivasa Ramisetti S.B.Ramisetti at leeds.ac.uk
Fri Jul 6 14:45:19 CEST 2018

Thanks Justin for the info. I understand that gmx distance -oh will produce the histogram for single pair of molecules. Since I want to generate histogram for several other combinations (96 in total) then I may have to call gmx distance several times which can be done through scripting. But I would like to know if there is any other approach like using gmx pairdist to generate the histogram for all pairs in one call.

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: 06 July 2018 12:47:21
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] histogram of distance between similar molecules

On 7/6/18 4:30 AM, Srinivasa Ramisetti wrote:
> Dear Gromacs users,
> I would like to know which tool (gmx distance or gmx pairdist) can be used to get a histogram (showing probability distribution function) of the centre of mass distance between similar molecules (14 molecules in total) for a range of time steps.

gmx distance -oh



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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