From: Benjamin Rousseau (benjamin.rousseau_at_duke.edu)
Date: Thu Aug 31 2017 - 10:31:31 CDT
I have seen this topic pop up a few times before, with mixed answers. I would like to understand the proper combination of the langevinHydrogen and the rigidBonds settings.
I have seen recommendations to set langevinHydrogen to off when using rigidBonds (http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2007-2008/2334.html)
as is done in many NAMD configuration files.
However, to my understanding, this removes the requirement that the average kinetic energy associated with each rotational degree of freedom of hydrogen must be ~ kT/2.
On the other hand, setting rigidBonds to all and langevinHydrogen to on imposes this requirement of KE=kT/2 for each degree of freedom of hydrogen. However, as one of the degrees of freedom is missing due to a rigid bond to a heavy atom, this results in a kinetic energy of ~ kT rather than ~ 3/2kT--_000_BLUPR05MB1906BBEF8D5B1B331221A9C2809C0BLUPR05MB1906namp_--
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