From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Wed Mar 07 2018 - 17:31:32 CST
As far as I can tell, there should be no problems with using HMR in NAMD as long as the hydrogen masses are no larger than 3. Is that right? I see in SimParameters.h the following:
> Bool ignoreMass; // Mass < 3.5 does not indicate hydrogen, etc.
suggesting that mass = 3.5 is the common threshold used to catch Hs (also seen elsewhere in the source code). So using one of the common approaches in which H masses go from 1 -> 3, NAMD should still catch them correctly. HMR is not applied to water typically, so I don’t foresee any problems with the fact that a reduced-mass oxygen (mass = 12) wouldn’t be recognized as such.
I just want to be sure I’m not overlooking anything. I tried it already and it ran fine, but there’s always the chance of a subtle error.
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