<font face="Arial, Helvetica, sans-serif">Hello All,<br>
I am trying to find interaction energy between 10 groups in a protein of 298 amino acids from a simulation run of 100ps.<br>
So I am expecting a 10x10 interaction energy matrix.<br>
I read the manual and found that g_enemat can generate this energy matrix.<br>
I defined the groups in the index (.ndx) file and rerun the simulation.<br>
Using the .edr in g_enemat and defining the proper groups in groups.dat I got an output like this as .xvg<br>
-----------------------------------<br>
@ title "Mean Energy"<br>
@ xaxis label "Residue"<br>
@ yaxis label "kJ/mol"<br>
@TYPE xy<br>
@ view 0.15, 0.15, 0.75, 0.85<br>
@ legend on<br>
@ legend box on<br>
@ legend loctype view<br>
@ legend 0.78, 0.8<br>
@ legend length 2<br>
@ legend string 0 "Coul-SR"<br>
@ legend string 1 "LJ-SR"<br>
@ legend string 2 "total"<br>
@ legend string 3 "Free"<br>
@ legend string 4 "Diff"<br>
@TYPE xy<br>
#grp Coul-SR LJ-SR total Free Diff<br>
1 -6.9294 -12.707 -19.636 -14.055<br>
2 -34.064 -22.729 -56.794 -56.898<br>
3 -22.528 -34.38 -56.908 -51.713<br>
4 40.298 -26.874 13.424 114.34<br>
5 -17.484 -24.832 -42.316 -41.51<br>
6 -13.843 -25.177 -39.02 -37.736<br>
7 -23.752 -19.644 -43.396 -41.401<br>
8 -31.425 -26.352 -57.777 -60.25<br>
9 -16.107 -19.686 -35.794 -24.935<br>
10 -26.014 -19.543 -45.558 -44.216<br>
<br>
---------------------------------------------------------------<br>
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 ?<br>
<br>
Thanks in advance<br>
Vijay<br>
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