hi, great.
I will leave comment about ParmEd to Jason.
Alternatively, you can use 'io' module in `pytraj` to read any supported
file types in cpptraj (`io.load` or `io.iterload`). This is example (just a
test file) showing the usage of pytraj with sander api (accept ParmEd
object too).
https://github.com/pytraj/pytraj/blob/master/tests/test_calc_energies_with_pysander.py
(this is python notebook:
http://nbviewer.ipython.org/github/pytraj/pytraj/blob/master/note-books/energy_decomposition.ipynb
).
hope this is useful.
cheers
Hai
On Sun, May 31, 2015 at 8:09 AM, Lee-Ping Wang <leeping.stanford.edu> wrote:
> Hi Jason and Hai,
>
> I’m just writing to follow up on the sander API. The code works very
> well! One minor note was that I used chemistry.amber.NetCDFTraj.open_old()
> in ParmEd instead of chemistry.load_file. The object returned by load_file
> does not have the frame attribute.
>
> Thanks so much. I think the sander API will be very interesting to work
> with.
>
> - Lee-Ping
>
> > On May 25, 2015, at 8:04 PM, Lee-Ping Wang <leeping.stanford.edu> wrote:
> >
> > Hai: Thanks a lot. I’ll see if I can get that to work once I get the
> data transferred, probably tomorrow because the data transfer is going to
> take a while. :)
> >
> > - Lee-Ping
> >
> >> On May 25, 2015, at 6:29 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >>
> >> .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
> >
>
>
>
> _______________________________________________
> 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 Sun May 31 2015 - 06:30:02 PDT
