Re: SHAKE or RATTLE algorithm

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.

-Dave

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?
>
> Both.
>
> >
> > 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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