[gmx-users] Potential energy coming out to be zero but not negative

Alex nedomacho at gmail.com
Fri Feb 23 19:57:45 CET 2018

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
> 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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