From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Fri Aug 05 2005 - 10:58:09 CDT
You can have shake on during minization, but it won't do anything since
the minimizer doesn't know about rigid bonds. You should probably have
shake on during equilibration if you're going to use it for dynamics.
There might be an argument that leaving shake off results in faster
equilibration due to the extra degrees of freedom, even though you need
shorter timesteps.
-Jim
On Wed, 3 Aug 2005, Stern, Julie wrote:
> I have a question about equilibration protocols. Is
> it typical that shake be off initially and then turned
> on later or is okay to have shake on for the whole
> minimization and equilibration process? Thanks for any
> opinions. (I know the amber people leave it off at first)
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:39:48 CST