Hi Adrian,
Have you looked into HMR with aMD?
Best,
Parker
On 3/16/15, 5:40 PM, "Adrian Roitberg" <roitberg.ufl.edu> wrote:
>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 - 15:30:02 PDT
