How is everybody doing the mass repartitioning? ParmEd? Their own
scripts? AFAIK ParmEd is the only way that is documented, implemented, and
included in the upcoming release. If I'm wrong somebody please correct me.
I don't know that ParmEd has worked its way into many peoples' standard
workflows so I'm not comfortable assuming everybody's using it to
repartition masses.
If people are using their own scripts to do this repartitioning I think it
is worth comparing against the "reference" implementation (preferably what
we're pushing on users) to make sure everybody's doing the same thing...
On Wed, Mar 12, 2014 at 3:23 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> our not-very-extensive study shows that all of the thermodynamic
> distributions that we've measured are within precision for 4fs vs 2fs, but
> there is notably greater tendency to crash in high T parts of REMD at 4fs.
>
>
> On Wed, Mar 12, 2014 at 3:17 PM, David A Case <case.biomaps.rutgers.edu
> >wrote:
>
> > On Wed, Mar 12, 2014, Adrian Roitberg wrote:
> >
> > > I agree with Scott
> > >
> > > When we started looking into this, my idea was that either
> > >
> > > a. it breaks, so we say bad things about other programs
> > > or
> > > b. it works, so we gain a factor of 2 in speed..
> > >
> > > a.
> >
> > So, is the final "a." your initial, or your choice between the two
> > alternatives listed above?
> >
> > Further, the "it works" might be true in a thermodynamic sense
> (==correctly
> > samples the Botzmann distrbution), or might also be true in a kinetic
> sense
> > (==rates of hopping among basins is roughly unchanged as well).
> >
> > ...dac
> >
> > _______________________________________________
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> >
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>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Mar 12 2014 - 14:00:02 PDT
