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.


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

Energy                      Average   Err.Est.       RMSD  Tot-Drift
Potential                -6.06412e+06    1.2e+06 5.52222e+07 -7.26522e+06

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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