Re: Hydrogen Mass Repartitioning in NAMD

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Thu Mar 08 2018 - 09:36:43 CST

Thanks guys. I saw that you (Brian) used it (but not the 4-fs time step) in the constant pH tutorial, so I figured it is probably safe* (for the solute, not the solvent). Glad to see that I didn’t overlook anything.

Best,
JC

*not legally binding; use at your own risk ;)

> On Mar 8, 2018, at 10:00 AM, Brian Radak <brian.radak_at_gmail.com> wrote:
>
> I might also add that I've also used ParmEd but with PSF format on the solute only.
>
> I've done a few benchmarks for energy conservation as well. If you want to be more conservative, you can do a 1-2-4 RESPA multistep integrator (bonded, nonbonded, full PME) with a 1 fs timestep. It's quite a bit slower but the energy conservation is much better. Then again, I've heard anecdotal reports that actual observables like PMFs don't show much variance at all, just as reported in the JCTC paper for AMBER.
>
> On Thu, Mar 8, 2018 at 9:53 AM, Norman Geist <norman.geist_at_uni-greifswald.de <mailto:norman.geist_at_uni-greifswald.de>> wrote:
> 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> [mailto: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 <mailto:namd-l_at_ks.uiuc.edu>>; JC Gumbart <gumbart_at_physics.gatech.edu <mailto: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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