OTOH if you guys find a conceptual hole in HMR, it would be extremely
useful for smacking the guilty parties (cough GROMACS cough AceMD) that
made adding it to AMBER a necessity with a spiked clue-by-4...
On Wed, Mar 12, 2014 at 8:34 AM, Adrian Roitberg <roitberg.ufl.edu> wrote:
> Hi all
>
> Please try it out! Make sure to use the proper scripts to get the new
> masses, do not just increase time step to 4 fs !
>
> We are writing a paper on this and will share it with everyone when we
> have a good draft.
>
> adrian
>
> On 3/12/14 9:55 AM, Thomas Cheatham wrote:
> >>> Note AMBER 14 will also support hydrogen mass
> >>> repartitioning so in principal you can run at 4fs time step.
> >> How much to we really know about this option? I've been playing with
> it for
> > We have been running a DNA 18-mer and also a RNA tetranucleotide r(GACC)
> > with h-mass repartitioning on the solute only and on everything. From
> > initial analysis, conformational distributions appear fairly identical
> for
> > the r(GACC), however we still need to look at kinetics, water properties
> > (viscosity should be higher), etc. When Christina, Ros and I get it
> > further analyzed, I'll summarize to the dev list...
> >
> >> Blue Waters (say) to run lots of simulations at 1, 2 and 4 fs time
> steps?
> >> Has anyone compared 2 and 4 fs where both have the mass repartitioning?
> > Ros/Christina, maybe we should fire up some more as per above. --tom
> >
> >
> > _______________________________________________
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> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
>
> --
> Dr. Adrian E. Roitberg
>
> Colonel Allan R. and Margaret G. Crow Term Professor.
> Quantum Theory Project, Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
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Received on Wed Mar 12 2014 - 10:30:02 PDT
