[gmx-users] trjcov - nojump

[K.A. Feenstra]

Rainer Boeckmann wrote:
> 
> I faced the problem (first occuring after some nanoseconds of
> simulation) that it was not possible to rewrite the trajectory with
> trjconv using the -pbc nojump option. It writes out broken molecules
> although I'm using a tpr-file without broken molecules. Does anyone have
> experience with that sort of problems?

'-pbc nojump' will only keep things together that were already together
to begin with, e.g. two subunits in a dimer. Also, it will only work
if the timestep between the frames is not excessively large, since it
has to check how much an atom moves in one step with respect to the
total size of the box. So if you have e.g. >100 ps steps (depending
on the type of system and molecule/s), this simple algorithm might 
simply break down... Whatever is in your topology file doesn't matter.


-- 
Groetjes,

Anton
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|        | Anton Feenstra                                            |
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