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

2018-02-24 Thread 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.markl...@kemi.uu.se

On 23 Feb 2018, at 19:32, 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+061.2e+06 5.5e+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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Re: [gmx-users] Potential energy coming out to be zero but not negative

2018-02-23 Thread Alex
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+061.2e+06 5.5e+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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