[gmx-users] core dumped during equilibration in gromacs

Mark Abraham mark.j.abraham at gmail.com
Wed Mar 22 11:41:15 CET 2017


All of the advice there still applies to trying to move from a successful
energy minimization to a dynamical simulation. Without knowing all the
details of how you prepared everything, that advice is all anybody can say.


> On Wed, Mar 22, 2017 at 11:08 AM ISHRAT JAHAN <jishrat17 at gmail.com> wrote:
> I have reduced the force and  timestep as given at http://www.gromacs.org/
> Documentation/Terminology/Blowing_Up
> <http://www.gromacs.org/Documentation/Terminology/Blowing_Up>
> <http://www.gromacs.org/Documentation/Terminology/Blowing_Up>  but still
> getting an error like-
> Double precision normally gives you higher accuracy.
> You might need to increase your constraint accuracy, or turn
> off constraints alltogether (set constraints = none in mdp file)
> writing lowest energy coordinates.
> Back Off! I just backed up prion_em.gro to ./#prion_em.gro.1#
> Steepest Descents converged to machine precision in 726 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  = -1.7322245e+05
> Maximum force     =  8.0706294e+03 on atom 2216
> Norm of force     =  1.4435008e+02
> if i proceed for pr with this result segmentation fault occured again.

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