[gmx-users] RMSD graph over time and g_cluster RMSD distribution seem at odds with each other
jalemkul at vt.edu
Wed Aug 13 16:17:50 CEST 2014
On 8/13/14, 10:11 AM, ms wrote:
> On 8/13/14 4:01 PM, Tsjerk Wassenaar wrote:
>> H Massimo,
>> The RMSD over time is the RMSD against a single reference structure. For
>> clustering you use the RMSD matrix, which has all pairwise RMSDs. The
>> distribution you show is the distribution of RMSD values in that matrix.
> Aha! This makes much more sense then, thanks!
> Is there a Gromacs command to get the histogram of RMSD against a single
> reference structure, then?
You can construct histograms of any time series with g_analyze -dist.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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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