> On Aug 7, 2020, at 2:52 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> On Thu, Aug 6, 2020 at 4:30 PM David A Case <david.case.rutgers.edu> wrote:
>>
>> [Amber developers: does anyone know which parts of the code still need to know
>> where the "molecules" are? I suspect we only have a molecular virial for
>> backwards compatibility with codes written 30 years ago, but I could be wrong
>> here -- I'm not really sure how the MC barostat works. Basically, I think
>> we have all these checks and atom-reorderings to deal with a problem that
>> really doesn't exist....]
>
> In order to do things like by-molecule imaging, cpptraj assumes
> molecules are contiguous. If they are not, all molecule-related stuff
> (imaging by molecule, 'closest', etc) is disabled. I suspect the
> molecule "wrapping" code in sander/pmemd might make this assumption as
> well, but I'm not sure.
This was definitely true before I went to my current job in 2016, but I’m pretty sure that code hasn’t changed in the last 4 years (it hadn’t in well over a decade prior).
Thanks,
Jason
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Fri Aug 07 2020 - 19:30:02 PDT
