AW: NAMD feature request Hydrogenscale

From: Norman Geist (
Date: Thu May 31 2012 - 01:09:59 CDT

Hi Maria,


in fact i don’t think it will create a mess. Why the default timestep is 1fs? Because it’s working stable. And why? Because all other parameters like rigidtolerance and rigiditerations and many other fits with that. So 1fs already is an approximation but it has been established for NAMD.


Also many people use multiple timestepping. What is better with that method?? Everybody knows it harms energy conservation critically.


The largest timestep with NAMD I can use is about 2fs without any thermostat or anything else special. Everything above will always crash for me.


The hydrogen mass repartitioning scheme is already used by gromacs and acemd and allows to simulate systems that needs long trajectories nearly 4 times faster. Also with better energy conservation than using fullelectfrequency 4 what many people need to do with NAMD on gpus.


Norman Geist.


Von: Maria Bykhovskaia []
Gesendet: Mittwoch, 30. Mai 2012 16:37
An: Norman Geist
Betreff: Re: namd-l: NAMD feature request Hydrogenscale


In your experience, what's the largest time-step you could use with NAMD, having a stable simulation? In my hands, 2 fs is always stable. The rattling problem also depends on thermostat. If I drop off Langevin and do velocity rescaling, I can go sometimes to 4 fs. That seems less drastic than artificially increasing hydrogen masses, although of course Langevin is preferable.

I only use 1 fs with external forces, and then I can't even even use Langevin and have to do rescaling. But when you simulate with external forces, playing with atomic masses may create a total mess.


On Wed, May 30, 2012 at 10:17 AM, Norman Geist <> wrote:

And of course a link to the publication of this method as it is already used.

Accelerating Biomolecular Dynamics in the Microsecond Time Scale

A little more serious please.
Why should I compute every timestep if I don't need it.

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: [] Im
> Auftrag von Vincent Leroux
> Gesendet: Mittwoch, 30. Mai 2012 15:04
> An:
> Betreff: Re: namd-l: NAMD feature request Hydrogenscale

> Focusing on the potential "scientific value" of making all hydrogens 4x
> heavier for the sake of getting MD "just run faster with big
> timesteps",
> how about passing the idea to the CHARMM forcefield developers in the
> dedicated mailing list? ;-)
> On 30/05/2012 14:14, Axel Kohlmeyer wrote:
> > On Wed, May 30, 2012 at 7:16 AM, Ajasja Ljubetič
> > <> wrote:
> >>> without commenting on scientific value,
> >>
> >>
> >> Could we hear this comment as well? (If it is not to vulgar, of
> course:)
> >
> > since i have no proper justification for
> > it, i'd rather not. the world is already
> > full of too many prejudices and people
> > with half-knowledge or no knowledge
> > blasting out opinions and speculations.
> >
> > axel.
> >
> >>
> >> Best regards,
> >> Ajasja
> >
> >
> >

Maria Bykhovskaia
Professor and Chair
Neuroscience Department
Universidad Central del Caribe
Bayamon, Puerto Rico <>

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