[gmx-users] g_cluster problem

Xavier Periole x.periole at rug.nl
Mon Feb 28 14:21:30 CET 2005

Andrew Beevers wrote:

>Dear all
>I am trying to produce the structure with the lowest RMSD difference to the others in the particular xtc file using g_cluster.
>The problem is that the protein is in a DMPC lipid bilayer and I cannot seem to do an RMSD comparison of just the protein structure without resulting in a output structure which has no bilayer.
>Is there any way of doing an RMSD comparison of just the protein structure whilst including its particular lipid environment (at that time point) in the final output structure?
>Any help would be much appreciated

The easy way around is to dermine the structure using g_cluster and then 
edit the trajectory (trajconc)
to extract (-dump xxx) the corresponding xxx structure, which then would 
include the lipids.



   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   Nijenborgh 4
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at rug.nl
   web-page: http://md.chem.rug.nl/~periole

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