I hope I'm not being out of line on this list, but this seems like a
suitable context to plug OpenMM. This kind of thing is exactly what OpenMM
is well suited for, and can be done from the Python, C, or Fortran
wrappers, or the C++ API itself. Relevant link in the python API
docs<
https://simtk.org/api_docs/openmm/api6_0/python/classsimtk_1_1openmm_1_1openmm_1_1Context.html#a4ce4ebac6ce95bd44e0d8c96d2f7229c>
Starting from the default script at
http://builder.openmm.org/, the only
modifications needed would be to to assign the implicit solvent force to a
separate force group and then get the state:
```
MYFORCEGROUP = 1
for i in range(system.getNumForces()):
force = system.getForce(i)
if isinstance(force, mm.GBSAOBCForce):
force.setForceGroup(FORCEGROUP)
[...]
state = simulation.context.getState(getEnergy=True, getForces=True,
groups=2**MYFORCEGROUP)
print(state.getForces(), state.getPotentialEnergy())
```
-Robert
On Mon, Mar 24, 2014 at 7:15 AM, Debayan Chakraborty
<debayan.ch.gmail.com>wrote:
> Dear Jason,
> Thank you for the information. I will definitely look
> through the NAB source code as well.
> Debayan
>
>
> On Mon, Mar 24, 2014 at 1:56 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > On Mon, 2014-03-24 at 13:41 +0000, Debayan Chakraborty wrote:
> > > Dear AMBER developers,
> > > I am interfacing a few of my
> > > subroutines with AMBER, and I need to call the subroutines which
> computes
> > > the GB energies and gradients. Can anyone please direct me to the
> > relevant
> > > sections of the code within the sander module.
> >
> > In the sander source directory: egb.F90
> >
> > You might have more luck working through the source code in NAB, though
> > ($AMBERHOME/AmberTools/src/sff/eff.c (the "REAL_T egb" function),
> > depending on your application.
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Tue Mar 25 2014 - 04:30:02 PDT
