Re: AW: NAMD feature request Hydrogenscale

From: Vincent Leroux (vincent.leroux_at_loria.fr)
Date: Wed May 30 2012 - 10:27:47 CDT

Excuse me, the fact that a method is published does not prevent me to
criticize it.

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?

This looks IMHO a little bit more serious than just changing atom masses
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

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...

Do you still think this is a good idea? If you wish, go ahead and ask
the CHARMM forcefield developers their opinion... this is especially
relevant since according to the Berendsen paper hydrogen mass
repartitioning only works well if piled up with dummy atoms usage,
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.
>
>> -----Urspr├╝ngliche 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 Ljubeti─Ź
>>> <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
>>>
>>>
>>>
>
>

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