[gmx-developers] Interfacing with gromacs to get potential energies/ forces

Augustin Chevallier augustin.chevallier at inria.fr
Fri Nov 18 11:43:47 CET 2016


first, I apologize if this is not the right mailing list, however it seemed more appropriate than user mailing list. 

I would like to get the potential energy computed by gromacs without having to use the command line and the overhead of writing/reading the result in files. I had a look at the code and indeed it seems possible using mdlib, however I'm a bit overwhelmed by the complexity of the code. 

>From what I understood, I should call the function do_forces(), however it has many parameters, and after looking at do_md() , mdrunner() and main() it seems there is quite a lot of things to set up before calling that function. 

So here are some more precise questions: 
*which initialization are required? should I just copy past some parts of mdrunner for that? 
*how do I load a gromacs topology file? 
*I guess I also need a forcerec, how do I create on too? 
*If I want to modify the atoms positions, can I do it in mdAtoms directly? 

I know these questions are rather vague, so if you could just point to which part of md_runner() and do_md() I should look at, it would greatly help! 

Augustin Chevallier 
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