On 2011-03-27 21.27, devicerandom wrote:
On 27/03/11 16:29, David van der Spoel wrote:
On 2011-03-27 16.42, devicerandom wrote:
Hi,
I am trying to use g_clustsize to follow aggregation of peptides. I am
currently using the following line:
g_clustsize -f my.trr -s ../my.tpr -nc nclusters.xvg -mol
Problem is, it actually counts monomers as clusters. I have a system
with 125 separate molecules, and the number of clusters starts from 125.
What can I do to indicate a minimum cluster size?
m.
What does it matter? Just simulate longer until you get two peptides to
aggregate. Check eg. maxclust.xvg.
Apologies, I've probably not been clear (I was writing in a rush, my
fault).
It matters because they aggregate nicely, but I want to follow the
number of *clusters* (that is, assemblies of 2 or more molecules) in
time (More precisely, I want to know the number of molecules within
aggregates).
Any hint? g_clustsize is a bit undocumented apart from the help page.
try the xpm files, and process those with xpm2ps
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
[email protected] http://folding.bmc.uu.se
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