Thank you very much, Hai! That resolved my issue. :)
- Lee-Ping
> On Feb 13, 2018, at 9:34 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> 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
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 13 2018 - 11:00:03 PST
