[gmx-developers] energy distribution

[David van der Spoel]

Robert Vacha wrote:
> Dear Developers,
> 
> I am interested in the calculation of the distribution of interaction
> energies between two groups (solute and solvent), not at the time but as
> number of molecules that interacts with certain strength. 
> As far as I know this is not implemented in Gromacs, so I would like to
> do that. I guess that it should not be so though because the
> interactions are calculated anyway. Is it right? And do you think would
> it be better to do it as modification of main run(where we can write
> this to energy file?) or would it be better to write a separate script
> that would run on trajectory file?

Let's try to make this a bit more specific: in principle you can compute 
an NxM matrix of interaction energies if you have N solute and M solvent 
molecules, or just an (N+M)^2 matrix. If you have fewer than 256 
molecules you can do this using energy groups. If you have more you will 
have to do some programming. The restriction of 256 energy group is due 
to the tpr file format not something in the code. What you want to do is 
the following:

- After reading in the tpr file give each atom in each molecule the 
molecule number as its energy group number.

Then you are done in principle and the energy matrix will be printed to 
the edr file. However if you have 10000 molecules this is no fun, as it 
will give you a 10000^2 energy terms. Better to build up the histogram 
within mdrun and save it separately. Then you probably want to treat 
identicle molecules as fermions, and group together all the same 
molecules. Now if you have Q different molecule types this will give you 
Q*(Q-1)/2 histograms. You can implement all of this using a flag to 
mdrun, and don't have to change any input files.

Together it seems like a week or two of work including debugging.

> 
> Many thanks for your time,
> best,
> Robert
> 
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-developers-request at gromacs.org.


-- 
David.
________________________________________________________________________
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++