[gmx-developers] request for trjconv -pbc pull_pbcatom

hessb at mpip-mainz.mpg.de hessb at mpip-mainz.mpg.de
Fri Feb 20 21:55:56 CET 2009


trjconv can already do this:
trjconv -center -pbc atom -ur compact
and then select one atom (the pbc atom) for centering.


> Hello,
> When applying the pull code and pulling something toward the center of
> mass of an aggregate of highly dynamic molecules (e.g. detergent
> micelle), the pull_pbcatom0 selection can be quite important, and yet
> it is not necessarily obvious if the box is sufficiently large, even
> for a smart selection of pull_pbcatom0. One could obviously just make
> the box larger, but it would be nice to avoid that.
> As an alternative, it would be nice to have an option to trjconv that
> functions exactly as the new pull code and outputs the periodic image
> of each atom that is closest to the selected pull_pbcatom. One could
> then view a long-time trajectory and empirically determine if the box
> is big enough for the study to be undertaken, or, more likely, run
> g_dist over all pairs and automate anomaly detection.
> I suspect that g_principal could be utilized here to determine cases
> in which the box is much too small, but I can't think of a tool that
> will detect small and infrequent problems.
> It is also unclear if the px or pf .xvg files from the pull code could
> be used to detect such problems, but I think that these would not
> catch the cases in which only a few atoms were put in the "wrong"
> image for COM determination.
> Thanks,
> Chris.
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