Dear Vitaly,
I had to struggle with the equilibration of an ionic liquid at charged
electrodes - it means a spatial inhomogeneous system and high forces due
to the electrostatics). I found the following tricks working for me:
* Pre-equilibration with a reduction of the step size (e.g. from 2 fs to
0.2 fs): After a several thousands steps (depends on the system of
course) the jobs can be restarted with the required time step simply by
using the .gro output file.
* Reducing the temperature and slowly heating the system by annealing.
* Don't use "generate initial velocities"!
* Assigning zero charges to some particles for the first equilibration
(E.g. in my case I had to charge the electrodes, which nearly always
crashed if I didn't to an equilibration before hand with neutral
electrodes. - Might be not useful in your case).
* Mixture of all steps above :)
I hope you will find some idea that helps you with the equilibration.
Regards
Kathleen
On 10/06/2012 07:27 PM, gmx-users-requ...@gromacs.org wrote:
Message: 3
Date: Sat, 6 Oct 2012 18:03:54 +0200
From: "Dr. Vitaly Chaban"<vvcha...@gmail.com>
Subject: [gmx-users] domain decomposition trick for highly parallel
non-equilibrium runs
To:gmx-users@gromacs.org
Message-ID:
<capxdd+z+_2wvvr4nv+ng84spgn362czmxjip1sgfezx5lk8...@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Dear all -
Would anyone perhaps suggest some tricks to increase the stability of
the highly parallel jobs (NP > 100), which use domain decomposition
among nodes. Especially, for the case, where beginning state of the
system is not equilibrium state (although it contains no bad contacts,
etc), i.e. the potential energy of the system decreases during MD.
Thank you for insights,
Vitaly Chaban
-- Dr. Vitaly V. Chaban MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy University of Southern
Denmark Campusvej 55, 5230 Odense M, Denmark
--
Kathleen Kirchner
PhD student
Max Planck Institute for Mathematics in the Sciences
(MPI f. Mathematik in den Naturwissenschaften)
Inselstr. 22-26, D04103 Leipzig
e-mail: kirch...@mis.mpg.de
web: http://www.mis.mpg.de/scicomp/CompPhysChem/
Tel +49 341 9959 725
Fax +49 341 9959 999
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