Re: [AMBER-Developers] hydrogen mass repartitioning

From: Thomas Cheatham <>
Date: Wed, 12 Mar 2014 07:55:46 -0600 (MDT)

> > 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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Received on Wed Mar 12 2014 - 07:00:02 PDT
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