[gmx-developers] Re: your kind advice needed

David van der Spoel spoel at xray.bmc.uu.se
Thu Mar 2 09:10:05 CET 2006

Marie wrote:
> Dear Sir
> I am intending to implement Hybrid Monte Carlo in Gromacs which simply
> collects energies (kinetic and potential) and accepts/rejects new
> coordinates based on total (kinetic + potential) energy using Monte Carlo
> test. If the new positions are failed, the old positions are restored and
> the momenta is regenerated randomly using gaussian distribution.
> My question is how easy would it be for me to get into the Gromacs code. I
> am not worried about the coding but about the dead ends where its not
> possible to implement such scheme into one integrator (HMC) and call MD
> integrator within it to make MD moves and perform what I described above. I
> have had bad experience with NAMD as its doesnt allow abstraction and
> flexibilty the way its integrator works so before I start my work on
> Gromacs, I would be really grateful to you for your kind advice.
> Many thanks for your time
> Marie
Hi Marie,

this is an interesting topic, and I'm sending this to the developers 
list as well, please subscribe and continue the discussion there. 
GROMACS has support for energy computation only, i.e. no forces as a 
variant of the normal code. It should be very efficient to do. Basically 
what has to be done is to replace the integration algorithm code in 
update.c, i.e. write a new "integrator" algorithm and call it from the 
update routine. The code is not abstract at the level that you might 
want, but it is not very complicated. If you want to have a complete 
implementation I presume you also would like to do pressure scaling 
(i.e. Volume moves) and things like that. Assuming you roughly know what 
you want to do, then please start by having a look at the update routine.

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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