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.
Chris. -- 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. Regards Kathleen -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
