Re: Hydrogen Mass Repartitioning in NAMD

From: Brian Radak (
Date: Thu Mar 08 2018 - 08:44:24 CST

One potential gotcha that I have not looked at thoroughly is HMR on water
molecules - fortunately, I don't think most people recommend this anyway.

I remember digging around the code and seeing that a repartitioned water
molecule might fail to get flagged as such because the *oxygen* mass would
be too *low*. This could goof up SETTLE.

Another tricky thing that I've seen people run into is that things like the
Langevin piston timescales may need to be re-adjusted to your timestep if
you are going up to 4 fs.


On Wed, Mar 7, 2018 at 6:31 PM, JC Gumbart <>

> Hi all,
> 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.
> Thanks!
> JC

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