[gmx-users] histogram of distance between similar molecules
jalemkul at vt.edu
Fri Jul 6 14:46:48 CEST 2018
On 7/6/18 8:44 AM, Srinivasa Ramisetti wrote:
> 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.
You can probably post-process the output with gmx analyze -dist, which
produces a histogram from whatever data you pass to it.
> 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
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Justin A. Lemkul, Ph.D.
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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