[gmx-users] periodic boundary trj

[Anton Feenstra]

David van der Spoel wrote:
> 
> 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
> trjconv.

That is already done. The option -pbc nojump in trjconv does exactly
what Giorgos asks: it will 'detect' an atom jumping from one side 
of the box to the other, and will re-set the coordinates to make a
continuous trajectory. However, it is atom based, which might not
be ideal in your case. '-pbc nojump -pbc whole' will definitely not
help you there (it won't be accepted), but running trjconv twice,
first using -pbc nojump and second using -pbc whole might work...

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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