[gmx-users] PBC problems when creating water layer around protein on an XTC trajectory

Marc Baaden baaden at smplinux.de
Wed Jul 27 18:03:28 CEST 2005


we are currently analysing some trajectories where we would like to look
at the hydration shell(s) of the simulated protein. We have already treated
the system with trjconv and trjorder to obtain the centered protein with its
20000 closest water molecules.

What troubles us is trying to get the "visually" correct water shell, which
is problematic because the protein is elongated, and using its center of mass
as reference point (as in -pbc cluster) does not systematically yield the
right periodic copy of the waters. In some cases one would want the water one
periodic box above or to the side. In fact to have the right result, several
periodic copies need to be considered.

The missing option in trjconv that could solve this would be :

 -pbc closest_to_any_atom_of_the_reference_group  (eg protein in our case)

because the com of the protein is not the right reference for the waters
at the edges.

How can this be done with Gromacs (or otherwise) on a whole trajectory ?
(I think for single frames one might be able to use genconf/genbox and
some tweaking)

Thanks in advance,

 BioMolSim meeting 2&3 Sep 2005: http://www.iecb.u-bordeaux.fr/satellite2005/

 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden at smplinux.de      -      http://www.baaden.ibpc.fr
 FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217

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