AW: Hydrogen Mass Repartitioning in NAMD

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Mar 08 2018 - 08:53:24 CST

I’m using it without problems with a timestep of 4fs for a long time already. I’m using Parmed and amber Parm7 files to apply the HMR. I recommend to scale the solute only, not the solvent.

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Brian Radak
Gesendet: Donnerstag, 8. März 2018 15:44
An: namd-l <namd-l_at_ks.uiuc.edu>; JC Gumbart <gumbart_at_physics.gatech.edu>
Betreff: Re: namd-l: Hydrogen Mass Repartitioning in NAMD

 

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.

HTH,

BKR

 

On Wed, Mar 7, 2018 at 6:31 PM, JC Gumbart <gumbart_at_physics.gatech.edu <mailto:gumbart_at_physics.gatech.edu> > wrote:

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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