[gmx-developers] interface for externally calculated forces
feenstra at few.vu.nl
Wed May 4 14:11:24 CEST 2011
On 04/05/11 12:34, Gerrit Groenhof wrote:
> On 05/04/2011 10:28 AM, David van der Spoel wrote:
>> On 2011-05-04 10.02, Rene Staritzbichler wrote:
>>> Dear Gromacs Team,
>>> I have been implementing an interface for external programs into an
>>> older version of Gromacs with the help of Gerrit Groenhof.
>>> The interface should allow to do these steps:
>>> - write atom coordinates into a xyz file
>>> - call an external program or script
>>> - read externally calculated forces, energy and virial from file and sum
>>> them to internally calculated ones
>>> Ideally one would have a line in the option file:
>>> external_forces = call.sh coordinates.xyz forces.dat
>>> Gerrit agreed that this would be of general interest and that it would
>>> be great to have it included into the main Gromacs release.
>>> Carsten from his lab mentioned that Gromacs is currently transferred to
>>> C++ and that I should ask here in this forum when it could be included.
>>> Best wishes,
>>> René Staritzbichler
>> Could this replace the QM-MM interfaces?
> It was in fact loosely based on the QM/MM interface
> Maybe it can replace the existing QM interfaces, provided some
> bookkeeping routines split up the QM and MM parts. Coming to think of
> it, the user could provide a script that calls the QM routine, scans the
> QM output and dumps a file with the forces in the rigth format. May make
> the QM/MM business a lot more simple.
A potentially more efficient option could be to use a callback function
of sorts, e.g. in python, which eliminates the file IO and system call
overhead. This could be based on the 'MD wrapper' (based on GromPy) that
René Pool developed in our group. See his earlier mails for details.
It isn't publicly available yet, but we can share the code with you.
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| _ _ ___,| K. Anton Feenstra |
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