I have calculated the binding free energy between a nanotube surface and protein by g_mmpbsa method. The polar solvation energy is coming out to be negative and approximately -1168 kJ/mol, due to this the total binding energy is highly negative approximately -2183.345 kJ/mol.
According to me this much of energy is not acceptable ideally I think?
My simulation length is also very long approximately half micro second. I run two more independent simulation of the same system. But in one simulation polar solvation energy is positive and in other it is negative.
Please suggest me something. What could be the reason behind negative polar solvation energy and is this energy is acceptable?
I am sharing summary_energy.dat file of one simulation here,
#Complex Number: 1
van der Waal energy = -1168.629 +/- 2.026 kJ/mol
Electrostattic energy = -3.769 +/- 0.191 kJ/mol
Polar solvation energy = -963.003 +/- 53.049 kJ/mol
SASA energy = -45.949 +/- 0.198 kJ/mol
SAV energy = 0.000 +/- 0.000 kJ/mol
WCA energy = 0.000 +/- 0.000 kJ/mol
Binding energy = -2183.759 +/- 54.315 kJ/mol
Kindly suggest me something. I shall be very thankful to all of you.
Thank you in advance.
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