I posted to the list a few days ago with an energy drift problem. Mark Abraham helpfully suggested using all-bonds rather than h-bonds which solved the problem. I'm now trying to understand quite why that helped so much.
The simulation is a protein of about 5000 atoms using GBSA, a time step of 2 fs, and a cut-off of 1.6 for VdW, coulomb and GB. I've run energy drift simulations using the md integrator, with no thermostat, and using the ld integrator with a tau_t of 1000000. Simulations were run changing various parameters. The changes were: - dt reduced to 1.5 - dt reduced to 1.0 - cutoff increased to 2.0 - constraint changed from h-bonds to all-bonds Plot of the energy drifts can be seen at http://www.reynwar.net/ben/gromacs/energy_drift.png. Noticeable features are: - changing the time step makes no difference (in my last post I claimed it did, which is why you should make plots rather than eyeballing log files). - increasing the cut-off helps a lot. - changing constraint to all-bonds make a dramatic difference - using ld there is a downwards drift in the energy when using all-bonds constraint. The temperature is roughly 300 K and the set point is 400 K so this downwards drift seems unlikely to be due to coupling to the langevin thermostat. My questions are: - why does the all-bonds constraint help so much? - why doesn't moving to a smaller time step help with this? - what is the cause of the downwards drift when using ld with all-bonds? Cheers, Ben -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
