Dear all,
I usually do not like doing this, but I think our recent paper would
benefit many of you.
Please take a look at pubs.acs.org/doi/abs/10.1021/ct5010406
"Long Time Step Molecular Dynamics through Hydrogen Mass Repartitioning
Chad W. Hopkins , Scott Le Grand , Ross C Walker , and Adrian E. Roitberg"
In this paper, we show how to manipulate the masses of atoms in Amber,
in order to be able to use a time step of 4 fs, while retaining the same
thermodynamic properties (and essentially the same kinetic properties)
as you would get when using regular masses and a dt=0.002
So, you gain a factor of 2x with a very small change.
If you use Parmed, you can use the HMassRepartitioning command to change
your prmtop to the 'new' masses, and then just change your mdin to dt=0.004
Please use it and report back successes and failures !
Thanks
adrian
--
Dr. Adrian E. Roitberg
Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Mon Mar 16 2015 - 15:00:03 PDT
