[gmx-users] Free Energy Landscape- PCA

Justin Lemkul jalemkul at vt.edu
Wed Dec 14 13:49:14 CET 2016

On 12/12/16 9:30 AM, Romero, Raquel wrote:
> Hi everyone,
> I have a number of trajectories over which I have conducted PCA using Gromacs. I have also generated a Free Energy Landscape using g_sham when the trajectory is projected along the PCs. I would like to know how I can extract the coordinates of those states of minimum energy shown in the FEL.

You'll need to find the corresponding frames by matching the eigenvalues from 
the time series.  Then you can dump out those frames using trjconv -dump.


> Thanks in advance,
> Regards
> Raquel Romero
> Department of Pharmaceutical and Biological Chemistry
> UCL School of Pharmacy, University College London
> 29/39 Brunswick Square
> London
> WC1N 1AX
> T: 0207 753 5972
> E: raquel.romero.12 at ucl.ac.uk


Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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