[gmx-users] g_enemat

[msvijayabaskar at aol.in]

Hello All,
I am trying to find interaction energy between 10 groups in a protein of 298 amino acids from a simulation run of 100ps.
So I am expecting a 10x10 interaction energy matrix.
I read the manual and found that g_enemat can generate this energy matrix.
I defined the groups in the index (.ndx) file and rerun the simulation.
Using the .edr in g_enemat and defining the proper groups in groups.dat I got an output like this as .xvg
-----------------------------------
@??? 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?? -6.9294?? -12.707?? -19.636?? -14.055
? 2?? -34.064?? -22.729?? -56.794?? -56.898
? 3?? -22.528??? -34.38?? -56.908?? -51.713
? 4??? 40.298?? -26.874??? 13.424??? 114.34
? 5?? -17.484?? -24.832?? -42.316??? -41.51
? 6?? -13.843?? -25.177??? -39.02?? -37.736
? 7?? -23.752?? -19.644?? -43.396?? -41.401
? 8?? -31.425?? -26.352?? -57.777??? -60.25
? 9?? -16.107?? -19.686?? -35.794?? -24.935
?10?? -26.014?? -19.543?? -45.558?? -44.216

---------------------------------------------------------------
Is this the matrix that g_energy promised ? Because I was expecting something like a 10x10 residue pairwise interaction energy. Can g_enemat program generate it ?

Thanks in advance
Vijay

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