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

Erik Marklund erik.marklund at kemi.uu.se
Sat Feb 24 17:41:31 CET 2018

Dear Shayantani,

The output you quote show a negative potential energy. Is that not for the run you refer to?

(With regards to “Hello Sir”, may I suggest a more gender inclusive greeting.)

Kind regards,
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>

On 23 Feb 2018, at 19:32, SHYANTANI MAITI <shyantani.maiti at gmail.com<mailto:shyantani.maiti at gmail.com>> 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

Best regards,
*Shyantani Maiti*
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