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
>>
>>
>>
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Received on Mon May 25 2015 - 20:30:02 PDT
