[gmx-users] trjconv -pbc

[Anton Feenstra]

Andre Farias de Moura wrote:
> hello rainer,
> 
> my tpr-file is ok, lipid molecules are not broken after
> "-pbc whole" option is applied. any other clue?

What interval do you have between the frames in your trajectory?
'-pbc nojump' relies on the distance 'traveled' between frames being
less than the half box length, so the asssumption can be made that
any 'jump' of more than half a box, must be artificial and will be
corrected. If you reduce a very long simulation to relatively few
frames (the numbers depend on the diffusion rate of your molecules),
this might not be appliccable.

For visualisation purposes, you might want to try '-pbc inbox'. That
will break molecules (all atoms are kept in the box), but gives a
'flat' interface at the box edges, which might look best. But that
will also depend on your rendering method of choice.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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