Hi All,
I am new to use this software. I have generated the energy_MM under this command:
g_mmpbsa -f traj.xtc -s topol.tpr -n index.ndx -mme -mm energy_MM.xvg -decomp -mmcon contrib_MM.dat -pdie 2
However the total binding energy is really high:
@ s0 legend "chA VdW Energy"
@ s1 legend "chA Elec. Energy"
@ s2 legend "chB VdW Energy"
@ s3 legend "chB Elec. Energy"
@ s4 legend "chA-chB VdW Energy"
@ s5 legend "chA-chB Elec. Energy"
@ s6 legend "chA-chB Total Energy"
0.000 0.000 0.000 0.000 0.000 -351.811 -1498.856 -1850.667
30.000 0.000 0.000 0.000 0.000 -300.090 -1366.446 -1666.536
60.000 0.000 0.000 0.000 0.000 -325.273 -1372.878 -1698.151
90.000 0.000 0.000 0.000 0.000 -334.094 -1435.629 -1769.724
However, if I used gromacs gmx energy, it gives me energy much lower and sensible:
Coul = -357.213
LJ = -136.393
Hence can someone explain to me why do I have such significant difference?
Best,
Ben