[gmx-users] -pbc nojump

[Mark Abraham]

On 20/10/2010 10:26 PM, shahab shariati wrote:
>
> Dear Mark
>
> you said in answer to -pbc nojump that using of new xtc file for 
> analysis section depends what one wants to observe.
>
> what observations is relevant to periodicity?
>

Anything that measures where something is relative to another. Normally 
one is only interested in the nearest periodic image. IIRC, some of the 
GROMACS tools are PBC-aware and determine the nearest suitable for 
themselves, other times they treat the trajectory as if there were no 
periodicity. In the latter case, if your results will be sensitive to 
the actual locations of atoms with respect to the periodic cell, then 
you'll wish to use trjconv to choose the configuration best suited to 
your needs. In the analysis desired the original post, the waters should 
all be in the same cell as the DNA+protein interstice, hence centering 
the cell on that group, and putting all waters into the cell.

Mark
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