Re: [AMBER] lj1264 in vacuum

From: Pengfei Li <>
Date: Sat, 16 Jan 2021 22:21:56 -0500

Hi Brian,

Maybe use sander to calculate the energy through the option imin=5 to process an existing trajectory? You can check the details about imin=5 in the AMBER manual.

Hope it helps,

> On Dec 11, 2020, at 4:07 PM, Brian Radak <> wrote:
> 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 <> 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 Sat Jan 16 2021 - 19:30:02 PST
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