[gmx-users] trjconv -pbc

[Anton Feenstra]

Rainer Boeckmann wrote:
> Hi Andre,
> 
> do you apply -pbc whole/-pbc nojump on the whole trajectory or only on snapshots
> or parts of the trajectory (with the initial tpr-file)? In the latter cases you
> might get broken molecules due to a change in box vector length. The nojump-flag
> uses the box parameters from the trajectory and not from the tpr-file. A
> solution would thus be to apply the procedure with whole & nojump on the whole
> trajectory (or on a small part with a changed tpr-file). trjconv -pbc nojump
> uses the tpr-file coordinates as a reference for the first frame but the box
> parameters from the first frame of the trajectory.

That doesn't sound quite right. If that is really the case, it might be a bug.
Can someone look into that?


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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