[gmx-users] Number of water molecules

Erik Marklund erikm at xray.bmc.uu.se
Fri Jun 6 22:14:09 CEST 2008

Marcelo Fabricio Masman skrev:
> Dear All.
> Is there any tool (or set of tools) in GROMACS which allows me to 
> calculate  #H2O vs time inside a pocket or in between two fragment of 
> a protein?
> Any help and/or hint will be fully appreciated.
> Marcelo
If you define an indexgroup for the pocket you could find the number of 
water molecules within any given distance with g_bond -contact. Between 
two protein fragments is a bit harder, because such a region is a bit 
ill defined.


Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys

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