[gmx-users] Warning in the em.

[João Henriques]

Dear Surya,

Which part of the text are you referring to? There's nothing particularly
wrong with it.

First paragraph is about not reaching the requested precision for the
maximum force, which may be due to the fact that it can't get any lower for
your system. This happens, and is not necessarily wrong.

Then you get a comment about how using double precision is meaningless when
prepping your simulation.

The final notes just point towards the fact that your minimization had an
imbalanced load between CPU and GPU. *If your PME settings are sound*,
there's not much to worry here. It only has consequences in terms of
performance, it doesn't affect the minimization *per se*. It just takes
longer to finish.

Finally, you have Arieh Warshel making what is, in my opinion, a silly
comment. But he won the Nobel, which sort of automatically validates
anything he says (just kidding guys!).

Best regards,
João

On Fri, Dec 4, 2015 at 10:24 AM, Seera Suryanarayana <palusoori at gmail.com>
wrote:

> Dear Gromacs Users,
>
> After my energy minimization I got the following info. I would like to know
> does it mean. I came to know that my em process is not perfect. Kindly tell
> me how resolve this problem.
>
>
> Energy minimization has stopped, but the forces have not converged to the
> requested precision Fmax < 1000 (which may not be possible for your
> system).
> It stopped because the algorithm tried to make a new step whose size was
> too
> small, or there was no change in the energy since last step. Either way, we
> regard the minimization as converged to within the available machine
> precision, given your starting configuration and EM parameters.
>
> Double precision normally gives you higher accuracy, but this is often not
> needed for preparing to run molecular dynamics.
> You might need to increase your constraint accuracy, or turn
> off constraints altogether (set constraints = none in mdp file)
>
> writing lowest energy coordinates.
>
> Steepest Descents converged to machine precision in 2297 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  = -1.8318672e+07
> Maximum force     =  2.9344773e+03 on atom 213
> Norm of force     =  8.8386917e+00
>
>
> NOTE: The GPU has >20% more load than the CPU. This imbalance causes
>       performance loss, consider using a shorter cut-off and a finer PME
> grid.
>
> NOTE: 15 % of the run time was spent in pair search,
>       you might want to increase nstlist (this has no effect on accuracy)
>
>
> gcq#384: "I do not believe continuum electrostatics" (Arieh Warshel, Nobel
> lecture 2013)
>
> Thanks in Advance
>
> Surya
> Graduate student
> India.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>