Oh, learning new things everyday. I actually subscribed to the maillist
when that particular thread was halfway thrugh. I have the last few post in
my inbox, did not make much sense when I received them. :)
Going back to the original subject, reported 239.14ns/day with amber is
also WITH hydrogen mass repartitioning. Match and win. Cool.
I don't think I will actually try that, though, it is very nice to know.
Now, about this comments-in-namelist thing..? No commenting, really?
Regards,
Murat
On Wed, May 14, 2014 at 10:33 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Wed, 2014-05-14 at 22:22 +0300, MURAT OZTURK wrote:
> > No, you need not say more (performance wise). :)
> >
> > Actually I was curious about the inner workings. The page you linked also
> > mentions 4 fs timestep. This is not recommended in amber (nor gromacs) as
> > far as I know. I mostly do 2 fs, sometimes even 1 fs timestep. If their
> > ns/day measurement is based on that, then it is off by %50. If they do
> > actually pull off a 4 fs timestep, then how?
>
> Hydrogen mass repartitioning -- they make the hydrogen atoms heavier and
> their attached heavy atoms lighter. For instance, a methyl group will
> go from
>
> 1.01
> |
> 1.01 -12.01 - 1.01
>
> to
>
> 3.00
> |
> 3.00 -6.01 - 3.00
>
>
> so that the total mass of the functional group stays the same but the
> heavier hydrogens vibrate with a (much) lower frequency. You still need
> to use SHAKE, but with the heavier mass the deviations are small enough
> for SHAKE to correct in a sensible number of iterations.
>
> Water constraints are solved analytically (SETTLE), so repartitioning is
> unnecessary there.
>
> You can do repartitioning in Amber using the ParmEd program (see the
> manual for details on the HMassRepartition command).
>
> Hope this helps,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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>
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Received on Wed May 14 2014 - 13:00:05 PDT
