wild guess:
> opts = sander.InputOptions()
->
> opts = sander.pme_input() # or something similar (don't have computer to
try it).
per document, there is a section in amber manual.
Hai
On Tue, Feb 13, 2018 at 10:31 AM, Lee-Ping Wang <leeping.ucdavis.edu> wrote:
> Hi there,
>
> I’m interested in asking pysander for the atomistic forces on my system
> (part of interfacing AMBER with ForceBalance). I think I have some options
> set incorrectly, because the electrostatic energy and forces are currently
> nan. These inputs and outputs come from a box of 1000 methanol molecules
> where I’ve already confirmed using sander / pmemd that MD simulations are
> fine.
>
> It’s worth mentioning that all of the energy terms match sander, except
> for the vdWaals term which is around -2360 in sander (only around -1000
> from pysander).
>
> Thanks a lot,
>
> - Lee-Ping
>
> PS: I can’t find the pysander documentation, so if anyone knows where it
> is please let me know.
>
> Input:
> -----
> #!/usr/bin/env python
>
> import sander
>
> inpcrd = sander.Rst7("amber-eq.restrt")
> opts = sander.InputOptions()
> opts.ntb=1
> opts.ntc=1
> opts.ntf=1
> opts.cut=8.0
> opts.igb=0
>
> sander.setup("amber.prmtop", inpcrd.coordinates, inpcrd.box, opts)
>
> e, f = sander.energy_forces()
>
> print("Bond", e.bond)
> print("Angle", e.angle)
> print("Dihedral", e.dihedral)
> print("Electrostatic", e.elec)
> print("Electrostatic 1-4", e.elec_14)
> print("Improper", e.imp)
> print("vdWaals", e.vdw)
> print("vdWaals 1-4", e.vdw_14)
>
> Output:
> -----
> Bond 310.39231708605456
> Angle 1837.9438528826322
> Dihedral 293.1245935416142
> Electrostatic nan
> Electrostatic 1-4 inf
> Improper 0.0
> vdWaals -1006.6764204631056
> vdWaals 1-4 -16.26494927531162
>
>
>
>
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>
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Received on Tue Feb 13 2018 - 10:00:02 PST
