[gmx-developers] Hybrid MC, accept/reject state

René Pool r.pool at vu.nl
Thu Feb 14 09:38:37 CET 2013

Hi Christian,

You may want to have a look at grompy 
(https://github.com/GromPy/GromPy). This is a python wrapper around the 
gromacs 4.0.7 library, using direct C-library calls. One current 
application is sampling the grand-canonical ensemble using a hybrid MC 

The application is published here:

Best regards,

René Pool

Department of Biological Psychology
Faculty of Psychology and Education
VU University Amsterdam
Van der Boechorststraat 1
1081 BT AMSTERDAM, the Netherlands

Room 2B-05
E: r.pool at vu.nl
T: +31 20 598 38 52

On 02/13/2013 05:01 PM, Christian H. wrote:
> Hi,
> I am trying to figure out how one would go about implementing a simple 
> Hybrid Monte Carlo scheme in GROMACS. For my purposes I am only 
> interested in the md-vv integrator, using either a NVT or NPT 
> ensemble. MPI is not a strict necessity, as the system I am going to 
> look at are probably small.
> So far I reversed the order between the energy calculation and the 
> trajectory output, by keeping a backup of my current configuration 
> where appropriate. This way I can check whether to accept the current 
> configuration before anything is written to the trajectory file.
> The point I am struggling with is the overall energy: It seems it is 
> not sufficient to just deal with enerd->term[F_ETOT] from md.c. For 
> example if I do an integration step, (thereby changing the current 
> enerd->term[F_ETOT]) and then decide to reject it (setting 
> enerd->[F_ETOT] = previousEnergy and copying back the previous 
> state->x), a different value than previousEnergy is written to the 
> .edr file.
> I guess the actual energy output takes place in print_ebin of 
> mdlib/mdebin.c, or more precisely do_enx of gmxlib/enxio.c. I can't 
> really make out of this works though. Is there any detailed 
> information about the file format available somewhere? It seems like 
> either enerd->term[F_ETOT] from md.c is not directly used and/or the 
> total energy is recalculated somewhere along the way.
> If anybody sees a glaring error in my approach in general, please 
> point it out as well - I am really new to the GROMACS source and have 
> only a rough understanding of how it works overall.
> Thanks,
> Christian

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