[gmx-users] Fw: minimization for final configuration

Justin Lemkul jalemkul at vt.edu
Tue Sep 30 16:37:50 CEST 2014

On 9/30/14 9:58 AM, Mahboobeh Eslami wrote:
> dear Justin
> thanks for your reply
> The plot of the RMSD against time for the trajectory generated with g_rms shows
> a maximum RMSD about 0.195 nm.
> I set cut-off value to 0.2 nm for g_clusters command.
> Is it a appropriate value?

g_rms and g_cluster do different types of RMSD evaluation.  g_rms compares 
against a single reference structure, g_cluster does RMSD between frames to 
decide on clusters, so the output of g_rms is not necessarily an indicator here. 
  You can tell for yourself whether or not the value was suitable by inspecting 
the loads of output that g_cluster provides you, and by visualizing the contents 
of the clusters to ensure that structures that were clustered together are 
reasonably similar.  For a structure that doesn't change much, you'll probably 
get one really big cluster and then a few that are sparsely populated.



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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