[gmx-users] g_cluster

[Nuno R. L. Ferreira]

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:

[...snip...]
"5 5 ... ..."
"A  c #FFFFFF " /*  "0"  */,
"B  c #.............  "/*   "0.0005"   */,
[...snip..]
/* x-axis:   1   2   3   4   5  */
/* y-axis:    1  2  3   4  5 */
"RPWFA"
"GHDAn"
"JHAnn"
"HAnnn"
"Annnn"

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

    1  2  3  4  5
5
4
3
2
1

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

Regards
Nuno
----- 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
Researcher
Department of Bioloigcal Sciences
University of Warwick

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