[gmx-users] g_clustsize

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Jun 13 15:08:27 CEST 2014

Hi Raisa,

I guess you know how many atoms are in a molecules, so you can divide the
clustersize in atoms by it to get the number of molecules. Probably the
biggest problem is that the output is in XPM format? I have a script
(attached) to convert that to generic .dat format, which you can then
process more naturally. Use as: ./xpm.py -f input.xpm -o output.dat

Hope it helps,


On Fri, Jun 13, 2014 at 2:55 PM, Raisa Kociurzynski <raisa_k at gmx.net> wrote:

> I can observe that GM1 molecules are separating from the DPPC molecules
> into GM1 domains. Is it possible to calculate the number of GM1 molecules
> in these GM1 domains? It worked with g_clustersize -cut 0.5 without the
> -mol option. I use the Martini force field.
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Tsjerk A. Wassenaar, Ph.D.

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