[gmx-users] Fw: minimization for final configuration

Mahboobeh Eslami mahboobeh.eslami at yahoo.com
Tue Sep 30 15:58:41 CEST 2014

dear Justin thanks for your replyThe 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?Sincerely.On Tuesday, September 30, 2014 2:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:


On 9/30/14 3:36 AM, Mahboobeh Eslami wrote:
> hi GMX users
> i have simulated the protein-ligand complex by gromacs for 20ns.
> The average for the final structure of 18 to 20 nanoseconds has been achieved.is minimization for the final average structure required?Sincerely.

An average structure might be totally unphysical.  Energy minimization of an 
unphysical structure leads you to something that is probably useless.  I'd 
suggest doing clustering if you're interested in the predominant conformation(s) 
during a certain time period of the simulation.



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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