[gmx-users] periodic boundary trj
David van der Spoel
spoel at xray.bmc.uu.se
Mon Mar 4 21:36:33 CET 2002
On Mon, 4 Mar 2002, Giorgos Karvounis wrote:
>I need to analyse the coordinates of solvent atoms but i face a problem
>with the periodic boundaries (the atoms jump from one box-wall to the
>other). Is it possible to change that , so as to get 'smooth'
>trajectories after the simulation has taken place?
This is implemented in g_msd to compute the mean square displacement (and
hence diffusion). In general it means your system would just evaporate,
and there is no tool that writes out a new trajectory.
You could however take the algorithm from g_msd and implement it in
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Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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