[gmx-developers] Help needed with hacking mdrun
feenstra at few.vu.nl
Thu Apr 7 14:55:28 CEST 2011
On 07/04/11 11:11, Semen Esilevsky wrote:
> Dear All,
> I need to hack mdrun in rather complex way and need some help from people, who
> understand Gromacs internals really well.
> My problem is the following. Each N MD steps I want to pass current
> coordinates and forces to custom function, which transforms them in a certain
> way (doesn't matter how at this point). Then I want to pass modified forces and
> coordinates back and continue simulation. Currently I got stuck with domain
> decomposition stuff. I figured out how to collect data on master node and pass
> it to my function. However, I have no idea how to distribute it back to all
> nodes correctly after modification.
A post-doc in our group, René Pool, has used the GromPy python interface
to implement a library interface to the mdrun integrator (mdrunner).
This library interface exposes the md datastructures, and makes it
trivial to do whatever coordinate transformations that you might
require, and then continue the simulation.
Please contact me or René (cc) off the list for more information.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | IBIVU/Bioinformatics - Free University Amsterdam |
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| | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/ |
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