On 12/15/16 10:02 AM, Romero, Raquel wrote:
Thanks a lot for your reply, Justin. That’s exactly what want but my problem is
that don’t know how, I mean, how can I know that correspondence? Getting that
correspondence is my only problem
You (presumably) constructed a time series of eigenvalues from gmx anaeig -proj
along PC1 and PC2, after which you constructed the free energy surface. That
means you have a time series of eigenvalues of those configurations projected
onto PC1 and PC2. So after you identify the bin in the 2-D surface that the
configurations fall, then you have a range of values to which those
configurations correspond. Then you just write a little script that parses the
PC1 and PC2 eigenvalue time series and when it identifies eigenvalues that
simultaneously fall inside the limits, print out the time value. Then apply
trjconv.
-Justin
On 14 Dec 2016, at 12:49, Justin Lemkul <jalem...@vt.edu> wrote:
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.
-Justin
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...@ucl.ac.uk
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==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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