I know it's bad form, but I'll give this a bump.
Is there a better forum for pysander questions?
On Tue, Dec 8, 2020, 4:29 PM Brian Radak <brian.radak.gmail.com> wrote:
> I'd like to test some C4 terms using the new-ish lj1264 option. It was
> easy enough to add new prmtop sections using ParmEd, but generating
> potential energy surfaces has been a bit harder. I attempted to use a
> combination of pytraj align/translate and pysander to generate scans of
> some non-bonded complexes, but things seemed to get weird.
>
> With standard inputs pysander (the pytraj.esander() function) seems to
> ignore LENNARD_JONES_CCOEF entries. I assumed this was because lj1264 =
> 0 and so I instead passed in pysander.gas_input() with lj1264 = 1. This
> apparently does not work either and the terms are ignored (which I guess
> I should have expected from the manual?), but the curves come out way
> differently (attached). If I instead use pysander.pme_input() with
> lj1264 = 1 then I can finally get the C4 terms to show up, but this may
> or may not exactly be what I want. I guess I can just play with cut and
> vdwmeth or use a huge box, but gas phase would be so much easier.
>
> Can anyone offer some suggestions here? Give up on pysander? Break into
> sander and implement lj1264 into the igb > 0 pathway? Something else?
>
>
> Thanks,
>
> Brian
>
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Received on Fri Dec 11 2020 - 13:30:02 PST
