Noone knows if you can continue your equilibration with this result, but
it has nothing to do with the sign of the total energy. In the case of
biomolecular forcefields involving quadratic energy terms for bonded
stuff, the sign of the total energy is meaningless. _Reduction_ in total
energy on EM is a correct trend. Do consult the manual for the energy
terms used in your forcefield.
Alex
On 2/23/2018 11:32 AM, SHYANTANI MAITI wrote:
Hello Sir,
When I go for energy minimization for a protein complex containing 3
proteins, I obtain potential energy being minimized upto zero from
positive. The potential energy is not becoming negative even after running
for many steps as viewed in potential.xvg obtained after energy
minimzation.
Energy Average Err.Est. RMSD Tot-Drift
------------------------------------------------------------
-------------------
Potential -6.06412e+06 1.2e+06 5.52222e+07 -7.26522e+06
(kJ/mol)
Is the energy minimization considerable for further equilibration or do I
need to obtain only negative energy and after that only should I start my
equilibration? Does the value of potential energy obtained after
minimization need to be negative in all cases? Can I continue my
equilibration with this result?
Thanking you
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