On Tue, Feb 13, 2018 at 12:32 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> 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.
>
>
You can see pysander example in pytraj:
https://github.com/Amber-MD/pytraj/blob/master/pytraj/analysis/energy_analysis.py
Hai
> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Tue Feb 13 2018 - 10:00:02 PST
