[gmx-users] Re: domain decomposition trick for highly parallel, non-equilibrium runs

Christopher Neale chris.neale at mail.utoronto.ca
Tue Oct 9 02:14:12 CEST 2012

Dear Kathleen:

It is important to either load velocities or generate them. If you do neither, then initial forces will rapidly be scaled up to thermally appropriate velocities, and if the initial forces are concerted, then you can get significant undesired concerted motion that can do things like partially unfold a protein.


-- original message --

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.


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