From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Fri Apr 04 2014 - 16:28:54 CDT
By default, NAMD constrains water using the SETTLE algorithm (non-iterative and faster) and constrains the bonds to the other hydrogens using SHAKE (iterative).
The RATTLE part of "SHAKE/RATTLE" for velocity-Verlet integration is simply a cosmetic fix to the velocity that turns out to be undone by the next time step. Since the overall dynamics are unchanged, NAMD skips that part of the algorithm.
On Apr 4, 2014, at 3:44 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Apr 4, 2014 10:26 PM, "Ramin Ekhteiari" <ramin_ekh_at_yahoo.com> wrote:
> > Hi,
> > Would you please let me know the algorithm used by NAMD code for restraining the bonds involving hydrogen atoms, is it SHAKE or RATTLE algorithm?
> > So appreciated for any advice
> > Cheers,
> > Ramin.
-- David J. Hardy, Ph.D. Theoretical and Computational Biophysics Beckman Institute, University of Illinois dhardy_at_ks.uiuc.edu http://www.ks.uiuc.edu/~dhardy/
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