Yes, should work.
Check that the central structures make sense. At some point this option was not
giving the correct structure.
On Jan 13, 2015, at 1:32 PM, Adriana Garro wrote:
> Another question just to be sure that I get what I want.
> I want the structure with the smallest average distan
Another question just to be sure that I get what I want.
I want the structure with the smallest average distance to the others (The
center of a cluster) for each cluster written in the clusters.pdb file
(option -cl), but after calculation I get this message in the log file
"Writing middle structu
Thanks for the reply Xavier.
Cheers,
Adriana
***
Dra. Adriana D. Garro
Química Medicinal
Facultad de Química, Bioquímica y Farmacia
Universidad Nacional de San Luis
IMASL-CONICET
San Luis, Argentina
Tel..:+54 266 4424689 int 61
with the gromos method the criteria is the RMSD between the structure of the
objects given to cluster …. two neighbours are two structures that are within
this cutoff (eg. 0.25)
obviously defining an RMSD between the two objects should make sense.
On Jan 12, 2015, at 4:56 PM, Adriana Garro w
Dear All,
I am working on a Coarse Grained model (Martini force field), I have a
trajectory file and
I am trying to do a clustering procedure using the gromos method, this is
the command line I used
g_cluster -f dynamic.xtc -s dynamic.tpr -o cluster.xpm -clid
cluster-id-over-time.xvg -cl clusters
