On Tue, Sep 22, 2015 at 8:26 PM, Sofia Vasilakaki <svasilak.chem.uoa.gr>
wrote:
> Hi to everyone,
>
> 1. Is there any example of a 'simple' python script to compute energies
> ect using OpenMM? What is the executable ? parmed.py ? There is no example
> in the manual. Any papers?
>
A lot of these questions deal with details of the OpenMM package which are
not particularly suitable for this list. OpenMM is a library, and there is
no executable to run it -- you have to write your own program or script to
do so. The Python application layer makes it easier, and parmed.py makes
use of the Python API to expose some OpenMM functionality within Amber.
Look at the documentation for the "energy" and "OpenMM" commands in the
manual -- those are the ParmEd actions that utilize the OpenMM API (the
first computes single-point energies and the second reads sander input
files and uses OpenMM to run simulations on either nVidia or AMD/ATI GPUs).
You can also find examples using ParmEd here:
http://parmed.github.io/ParmEd/html/openmm.html
If you have specific questions about ParmEd, feel free to ask them here.
If your questions are about OpenMM, however, then the OpenMM forum is the
appropriate place to seek help (both because few people that answer
questions here know OpenMM well enough to help and because people with the
same question in the future will likely search the OpenMM archives for
previous questions/answers). See
https://simtk.org/forums/viewforum.php?f=161
>
> 2. Is the energy results of OpenMM comparable with MMPB(GB)SA? Can I use
> them in order to double check MMGBSA results?
>
The energy results are very comparable and usually give you <1 kcal/mol
agreement in energies and much better agreement in the forces. But using
it to double-check MMGBSA results is only useful as an educational exercise
to learn some advanced tricks in OpenMM. This is *far* more challenging
than simply using OpenMM to run a MD simulation. (And since the GB models
in OpenMM were validated against Amber results, it is highly unlikely you
will get different answers).
If you really want to double-check the MMGBSA results, you should do it *by
hand* with sander (since MMPBSA.py uses nab by default).
HTH,
Jason
>
> Thank you in advance,
> Sofia V.
>
>
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--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Sep 23 2015 - 06:30:03 PDT
