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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Received on Wed May 14 2014 - 13:00:04 PDT
