[gmx-users] g_enemat

[Mark Abraham]

>
> Hi All
>
> I am trying to get the interaction free energy
> between a single solute and solvent to calculate the solvation free energy
> finally.
> For that, I ran a 10 ns trajectory of an NpT ensemble with two separate
> energy groups (solute and solvent).
> The output file from the g_enemat tool looked as following;
> **********************************************************
> # This file was created Thu Jul  5 10:42:39 2007
> # by the following command:
> # g_enemat -f rerun.edr -groups groups.dat
> #
> # g_enemat is part of G R O M A C S:
> #
> # GROningen MAchine for Chemical Simulation
> #
> @    title "Mean Energy"
> @    xaxis  label "Residue"
> @    yaxis  label "kJ/mol"
> @TYPE xy
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ legend string 0 "Coul-SR"
> @ legend string 1 "LJ-SR"
> @ legend string 2 "total"
> @ legend string 3 "Free"
> @ legend string 4 "Diff"
> @TYPE xy
> #grp   Coul-SR     LJ-SR     total      Free      Diff
>   1    -19973    -33241    -53214       inf
>   2    -135.2    -41506    -41641       inf
>
> *********************************************************
>
> Here I am having a little trouble in interpreting the results shown above.
> Since I am interested in the interaction energy between the two groups,
> I expected to get a single value for each different energy term.
> Instead I got values for two groups separately, and,
> furthermore, the value for the free energy was inf (might be inifite).
>
> Could someone help me how I can interpret the data?
> Or should I change some thing to get the right answer?

You don't appear to have read the man page for g_enemat, else your command
line would be different. I've never used g_enemat and already I seem to
know how to calculate the "interaction energy between the two groups" just
from that simple step. Also, since you haven't supplied the contents of
groups.dat, anybody who knows enough about g_enemat to help you has little
opportunity to do so. Check out
http://www.catb.org/~esr/faqs/smart-questions.html to learn how to get
useful feedback from lists like this one.

Mark