[gmx-users] RMSD graph over time and g_cluster RMSD distribution seem at odds with each other

Justin Lemkul 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
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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