[gmx-developers] Terminate simulation depending on distance condition

Leonhard Heizinger Leonhard.Heizinger at ur.de
Fri Jan 26 17:20:21 CET 2018

Hi GROMACS devs,

it would be great if it was possible to terminate a GROMACS run when a
certain distance condition isn't satisfied anymore. In my case I'm
simulating a protein-ligand complex.
I want to terminate the simulation when the ligand leaves the binding

I'm currently trying to get a quick'n'dirty implementation working:
* Periodically check distance in condition in the
do_md_trajectory_writing function (gromacs/mdlib/trajectory_writing.cpp)
* Set a flag if the condition isn't satisfied anymore
* Terminate the MD run by checking the flag in programs/mdrun/md.cpp
* Add a new command line option to md_run to let the user define the
distance condition

Adding an additional stop condition to md.cpp works fine already.
However I'm stuck with calculating the distance in do_md_trajectory_writing.
Is it possible to reuse the distance calculation code in distance.cpp?
Maybe somebody has already done something similar?


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