[gmx-users] g_enemat

이선주 sunnytov at hotmail.com
Thu Jul 5 18:18:55 CEST 2007

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?

Thank you in advance

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