[gmx-users] Energy Drift
ben at reynwar.net
Tue Oct 18 23:03:40 CEST 2011
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
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?
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