[gmx-developers] Modifying the GROMACS Integration algorithm

David van der Spoel spoel at xray.bmc.uu.se
Sat May 26 19:03:08 CEST 2007

Nava Whiteford wrote:
> Hi,
> I'm am looking for an MD code to test a new integration algorithm with, I 
> was wondering if anyone could point me in the direction of the main 
> integration loop in GROMACS or perhaps give some insight in to how easy 
> this might be to accomplish with GROMACS.
> I have previously tried to modify NAMD but ran in to trouble when trying 
> to perform two force calculations in a single timestep, does anyone know 
> if this would be a difficult modification to make with GROMACS as well?
> Any help appreciated,
> Nava Whiteford
Go to src/kernel/md.c and look in md.c
then you see that calls are made to do_force (src/mdlib/sim_util.c) and 
update (src/mdlib/update.c).

Of course the devil is in the detail since the integration algorithm 
also calls constraint routines and does temperature and pressure 
coupling. It might be better to roll your own little program that only 
does argon, and once you have the math correct in your own program you 
start porting it to a big package like GROMACS.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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