.Lee-Ping: if you ever want to use `pytraj` with `sanderapi` and `ParmEd`,
you can in-the-fly (easily) play with single temperature frames from T-REMD
run without writing to temperature-trajectory first (thanks to cpptraj's
smart indexing).
http://nbviewer.ipython.org/github/pytraj/pytraj/blob/master/note-books/load_remd_traj.ipynb
Hai
On Mon, May 25, 2015 at 4:43 PM, Lee-Ping Wang <leeping.stanford.edu> wrote:
> Hi Jason,
>
> Thanks for the suggestion. I agree I could keep the water and use the
> sander API to compute the energies.
>
> - Lee-Ping
>
> > On May 25, 2015, at 12:12 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
> >
> > On Mon, May 25, 2015 at 12:44 PM, Lee-Ping Wang <leeping.stanford.edu>
> > wrote:
> >
> >> Hi everyone,
> >>
> >> I’ve been running some replica exchange simulations in Amber. I’ve got
> a
> >> simple script for cpptraj (adapted from the tutorial at
> >> http://ambermd.org/tutorials/advanced/tutorial7/ <
> >> http://ambermd.org/tutorials/advanced/tutorial7/> ) for processing the
> >> output trajectories, resulting in “temperature-based” trajectories where
> >> the temperature is constant but the conformations jump around. The
> >> simulations are running very nicely; thanks for writing a great software
> >> package.
> >>
> >> My question is how I could get potential energies to “go with” these
> >> trajectories? I would like to use these potential energies as input to
> a
> >> WHAM / MBAR calculation to improve the estimation of thermodynamic
> >> properties at each temperature.
> >>
> >
> > The standard way is to feed those trajectories into sander, set imin=5
> to
> > process an input trajectory, and get energies that way. But I'll provide
> > an alternative I think you may find more amenabl
> > e:
> >
> > Use the sander API to compute single-point energies (and assuming you're
> > going to turn around and feed this directly into pymbar, you can do
> > everything you want in a single script). You can do something like this:
> >
> > import sander
> > import chemistry as chem
> >
> > parm = chem.amber.AmberParm('prmtop', 'inpcrd')
> > traj = chem.load_file('your_trajectory') # mdtraj or pytraj also works to
> > read trajectories
> >
> > input = sander.pme_input() # or use "gas_input(NUM)" where NUM is the igb
> > model for implicit solvent
> > input.cut = 9.0 # struct members have same name as mdin variables
> >
> > with sander.setup('prmtop', parm.coords, parm.box, input):
> > for i in range(traj.frame):
> > sander.set_positions(traj.coordinates(i))
> > ene, frc = sander.energy_forces()
> > # Go ahead and store your potential energy in a numpy array you
> set
> > up
> >
> > You can also use OpenMM instead of the sander Python API if you're more
> > comfortable with that.
> >
> >
> >
> >> My simple script is attached below.
> >>
> >> Thanks,
> >>
> >> - Lee-Ping
> >>
> >> parm ../prmtop
> >> ensemble ../remd.00/netcdf.00
> >> ensemble ../remd.01/netcdf.00
> >> ensemble ../remd.02/netcdf.00
> >> strip :WAT
> >>
> >
> > Obviously you can't calculate the full energies if you strip waters,
> but I
> > figured I'd point this out anyway.
> >
> > All the best,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> > _______________________________________________
> > 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 Mon May 25 2015 - 18:30:03 PDT
