[gmx-users] g_cluster

Nuno R. L. Ferreira nunolf at ci.uc.pt
Fri Mar 18 18:34:11 CET 2005

What about the .xpm file obatined with the -o flag? You have for each
combination, a RMSD value. Search for the minimum in the x-pixmap ascii
file. Ignoring the identity combinations (same structure I mean), search the
combinations which is assigned the "B" character. The "A" char means RMSD=0.

e.g. you have 5 structures you want to cluster
your .xpm file will be something like:

"5 5 ... ..."
"A  c #FFFFFF " /*  "0"  */,
"B  c #.............  "/*   "0.0005"   */,
/* x-axis:   1   2   3   4   5  */
/* y-axis:    1  2  3   4  5 */

If I'm not mistaken, the order of the structures in the .xpm file is:

    1  2  3  4  5

Yep, that's it.
Search for the combinations which have the char with the lowest RMSD.

----- Original Message ----- 
From: "Andrew Beevers" <A.J.Beevers at warwick.ac.uk>
To: <gmx-users at gromacs.org>
Sent: Friday, March 18, 2005 11:57 AM
Subject: [gmx-users] g_cluster

Hi All

Is there any output form g_cluster which states the time-step of the
selected lowest RMSD structure?
Thankyou in advance

Andy Beevers

Dr Andy Beevers
Department of Bioloigcal Sciences
University of Warwick

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