[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:

>Dear all,
>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

>Kind Regards,
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Groeten, David.
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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