Dear Amber community,
I’ve been testing out the effect with different gamma_ln values (0.1, 2, 5, 10) using a Langevin thermostat, and what I found with my system (NPT, using ntf=7 only evaluating non-bonded forces, giving my protein a weight restraint of 100 so that it’s as fixed as possible) was that different random seeds with the same gamma_ln give very close average energies from the MD output (-75000+-5), while different gamma_ln values give different average energies(-75000+-500). The runs are over 100 ns and the averages seemed to be converged pretty well within each gamma_ln value, while they are systematically different between different gamma_ln.
Is this difference in energy expected? Because it’s undesired for my tests here. Could it be something specific with my system that’s causing this?
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jan 16 2021 - 18:00:02 PST
