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[Anton Feenstra]

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.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| 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"           |
|             | (Red Hot Chili Peppers)                               |
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