[gmx-users] channel size calculation between active site lid

Serge Yefimov s.yefimov at rug.nl
Thu Aug 10 13:41:09 CEST 2006

You can use program called HOLE: http://d2o.biop.ox.ac.uk:38080//, it 
can calculate the pore profile of your channel.

raja wrote:
> Hi all,
> I followed center of mass (COM) between lids region (two loops covering
> the entrance of active site) during simulation to see its action of
> opening and closing. Normally COM varies for all simulation of my
> protein (Wild and its mutant variant) is between 17A to 20A. Now I want
> to find out the average opening size (Pore or channel size) during
> simulation through which the substrate believed to reach the active
> site. How to do it either within or outside of gromacs?
> With thanks!
> B.Nataraj

Serge Yefimov

University of Groningen
Department of Applied Physics
Micromechanics of Materials
Nijenborgh 4, 9747 AG Groningen
The Netherlands

tel: +31-50-3634835
fax: +31-50-3634886
e-mail: s.yefimov at rug.nl

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