feenstra at chem.vu.nl
Fri Jul 23 17:45:57 CEST 2004
Raghunadha Reddy Burri wrote:
> Dear GMX users,
> In my simulation of protein and water frequently going out of cubic box!
> Periodic boundary conditions in all directions means no more out of box
> ( because every side have another box same as current box) but really I do
> not understand how some of simulation frames showing protein (some time water
> also) going out of box, this is really getting problem to make a movie from
> trajectory file.
> How can possible to maintain protein in cubic box?
mdrun handles pbc by keeping *molecules* in the box (or, rather, the
first atom of each molecule), which means that several (or many) atoms
of a molecule can be out of the box. trjconv has several alternate
options to treat pbc, type 'trjconv -h' and look for the '-pbc' option.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" |
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