<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Hi santhu,<br>
maybe the differecence you observed depend by the xpm format. <br>
In the xpm each cell is represented by one character that, in turn,
is represented as a color by xpm2ps. <br>
Therefore the character count cannot be infinite so each character
can represent a range of RMSD cell.<br>
In my opinion this rapresentation is the source of the problem.<br>
<br>
You should modify g_cluster to write the RMSD matrix in a binary
format to avoid rounding error and,<br>
at the same time, to save computational time.<br>
<br>
Il 29/09/2011 22:25, santhu kumar ha scritto:
<blockquote
cite="mid:CA+7TRsvpv3aBZr_n58ARApMZNModYbyCAyBC4=xjR0CkOpB+kQ@mail.gmail.com"
type="cite">Hello,<br>
<br>
I am using g_cluster to cluster trajectories. <br clear="all">
The exact command I am using is : g_cluster -s protein.pdb -f
all.trr -n index.ndx -o rmsd-clust.xpm -method gromos -cutoff 0.07
-wcl 250. This command gives me 145 clusters. <br>
<br>
This command writes out a rmsd-clust.xpm, which is the RMSD
distance matrix. Since the trajectory is quite huge, i want to
perform the RMSD matrix computation only once.<br>
If I want to change options of clustering, I have tried giving the
computed matrix as input to another run but the results are quite
different. <br>
<br>
For example : g_cluster -s ubqs.pdb -f all.trr -n index.ndx -dm
rmsd-clust.xpm -method gromos -cutoff 0.07 -wcl 250 would then
give only 3 clusters. <br>
<br>
Can somebody please advice me on how to avoid recomputing the RMSD
distance matrix for each change in clustering option??<br>
<br>
Thanks<br>
Santhosh<br>
<br>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</body>
</html>