From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu May 31 2012 - 01:06:29 CDT
> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Vincent Leroux
> Gesendet: Mittwoch, 30. Mai 2012 17:28
> An: namd-l_at_ks.uiuc.edu
> Betreff: Re: AW: namd-l: NAMD feature request Hydrogenscale
>
> Excuse me, the fact that a method is published does not prevent me to
> criticize it.
Hopefully not. No opinion, no progress.
>
> Well, if you do not want to compute more timesteps than required, then
> why don't you use r-RESPA-based multiple timestepping (nonbonded 2 and
> fullelectfrequency 4 can work very well on your typical protein-protein
> or protein-ligand system provided careful equilibration was done) and
> the Molly method as recently implemented in NAMD?
I'm already using fullelectfrequency 4 for better speedup through the gpus, but that harms my energy conservation and my system increase temperature by about 0.5K-1K per ns.
>
> This looks IMHO a little bit more serious than just changing atom
> masses
Question of philosophy. I don't think calculating non-bonded and electrostatic forces with atom positions that are no more true is better.
> while using a forcefield that was not parameterized against these new
> unnatural values. In the reference you provide, it is just mentioned
> such a trick only moderately affects the viscosity in a TIP3P water
> box,
> you have to go to the original reference from the people that actually
> had the idea to get some serious validation attempts:
> http://dx.doi.org/10.1002/(SICI)1096-987X(199906)20:8<786::AID-
> JCC5>3.0.CO;2-B
Please read more carefully. The viscosity change of the water was a side effect, not the effect that was targeted.
>
> You will see that the gain in performance is not so high, without
> resorting to additional tricks, and that the effect of the dynamical
> behavior of the simulated system is not negligible...
That's not true. Without additional tricks a timestep of 4fs is possible only with the hydrogen mass repartitioning, 4 times higher than namds default 1fs.
>
> Do you still think this is a good idea? If you wish, go ahead and ask
Yes.
> the CHARMM forcefield developers their opinion... this is especially
In fact I use the amber ff.
> relevant since according to the Berendsen paper hydrogen mass
> repartitioning only works well if piled up with dummy atoms usage,
Not true. This only provides the possibility of even higher timesteps than 4fs.
> requiring some additional tinkering with the force field itself, so
> that
> the dihedrals are not messed up... So you need a kind of forcefield
> able
> to tolerate that. That would certainly be more GROMOS than CHARMM.
>
> Regards
> VL
>
>
> On 30/05/2012 16:17, 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
> > http://pubs.acs.org/doi/full/10.1021/ct9000685
> >
> > A little more serious please.
> > Why should I compute every timestep if I don't need it.
> >
> > Norman Geist.
> >
> >> -----Ursprüngliche Nachricht-----
> >> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> >> Auftrag von Vincent Leroux
> >> Gesendet: Mittwoch, 30. Mai 2012 15:04
> >> An: namd-l_at_ks.uiuc.edu
> >> 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
> >>> <ajasja.ljubetic_at_gmail.com> 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
> >>>
> >>>
> >>>
> >
> >
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:35 CST