[gmx-users] jumps through the box

[K.A. Feenstra]

Rainer Boeckmann wrote:
> Dmitry Kovalsky wrote:
> 
> 
>>Hi
>>
>>My protein consists of two chains and when I perform long simulation and it
>>moves toward box edge one subunit begans jumping.
>>
>> I have tried like  here was suggested
>>http://www.gromacs.org/pipermail/gmx-users/2002-June/001899.html
>>This helps but only in part: the two monomers are "reconnected" but now the
>>whole protein jumps.
>>
> 
> 
> after the trjconv -whole you should apply trjconv -nojump. that will keep the
> molecule whole AND remove jumps.

In that case, '-whole' is not necessary, simply using '-nojump' will keep
everything together like it was in the beginning.

But, there is not really a 'problem': all gromacs analysis programs will recognize
the periodicity of the system. If you want to look at the trajectory without
having your molecules jump around, you might also want to put them in the
center of the box (use 'trjconv -center').


-- 
Groetjes,

Anton
  ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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