[gmx-users] cluster analysis on HREX results

Shyno Mathew sm3334 at columbia.edu
Fri Oct 16 14:19:25 CEST 2015

Dear all,

1. For the cluster analysis, I am using the gromos method with cutoff 0.25
With this cutoff I got 201 structures for the lowest temperature for
trajectories that are continuous in time (after using demux.pl)
The rmsd ranges from 0.073 to 1.55nm.

If I reduce the cutoff to 0.1 nm I will get 1919 structures, which is very
close to the total number of frames, 2001 in the .xtc file. This doesn't
make sense as I am getting one structure for each frame. Here 1 frame
corresponds to 0.01 ns

My question, with the cluster analysis, do you fix the value of cutoff or
you change cutoff to get a certain number of structures?

Following is the syntax I used:
 g_cluster_mpi -s PRO0.gro -f redPRO0.xtc -method gromos -sz clustsize0.xvg
-o clusters0.xpm -g cluster0.log -clid clusidovertime0.xvg -cl out0.pdb
-cutoff 0.25

2. For replica exchange,is it better to do the cluster analysis on
trajectories that are continuous in ensemble or trajectories that are
continuous in time (after using demux.pl)
I tried both ways:
For replica 0 (for trajectories that are continuous in ensemble, at lowest
temperature 300 K), I got two structures with cutoff 0.25
For replica0 (for trajectories that are continuous in time), I got 201
structures with cutoff 0.25

Thanks in advance for your help.

Shyno Mathew
PhD Candidate
Department of Chemical Engineering
Graduate Assistant
Office of Graduate Student Affairs
The Fu Foundation School Of Engineering and Applied Science
Columbia University

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