[gmx-developers] request for trjconv -pbc pull_pbcatom

[chris.neale at utoronto.ca]

Fantastic,

Thanks Berk. I didn't realize that this was the same behaviour.

Chris.

Quoting hessb at mpip-mainz.mpg.de:

> Hi,
>
> trjconv can already do this:
> trjconv -center -pbc atom -ur compact
> and then select one atom (the pbc atom) for centering.
>
> Berk
>
>> 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.
>>
>> _______________________________________________
>> gmx-developers mailing list
>> gmx-developers at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-developers
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-developers-request at gromacs.org.
>>
>> --
>> This email was Anti Virus checked by Astaro Security Gateway.
>> http://www.astaro.com
>
>
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-developers-request at gromacs.org.
>