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

[Erik Marklund]

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
______________________________________________
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
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

--
Best regards,
*Shyantani Maiti*
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