[gmx-users] Fwd: problem in energy minimization

[Mark Abraham]

Hi,

That could be fine, as your potential energy is large and negative. We
can't tell from the outside. Do visualise the before and after to get some
clues.

Mark

On Tue, Jul 17, 2018, 19:11 neelam wafa <neelam.wafa at gmail.com> wrote:

> ---------- Forwarded message ----------
> From: neelam wafa <neelam.wafa at gmail.com>
> Date: Tue, Jul 17, 2018 at 1:12 PM
> Subject: problem in energy minimization
> To: gromacs.org_gmx-users at maillist.sys.kth.se
>
>
> Hi,
>
> Dear gromacs users, I am running md simmulation of a protein with a ligand.
> i have already done it with the same protein and a different ligand. Now
> when i run em md run i get following result.
>
> 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 150 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  = -9.3659806e+05
> Maximum force     =  1.0269271e+04 on atom 4399
> Norm of force     =  9.8929054e+01
>
> NOTE: 10 % of the run time was spent in pair search,
>       you might want to increase nstlist (this has no effect on accuracy)
>  please guide me is it reliable to proceede for simmulation. or there is
> something wrong. Is it a sign of system instability?
>
> looking forward for your cooperation.
>
> Regards
> --
> 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.
>