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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Received on Tue Feb 13 2018 - 08:00:04 PST
