Date: Tue, 8 Dec 2020 16:29:25 -0500
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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