AMBER Archive (2008)

Subject: Re: AMBER: velocity-verlet algorithm and ensembles

From: David A. Case (
Date: Thu Oct 09 2008 - 07:46:08 CDT

On Wed, Oct 08, 2008, oguz gurbulak wrote:

> I want to use velocity-verlet algorithm for my MD simulations. And I
> searched Amber manuals and Amber mail archive in order to get more
> information about using velocity-verlet ( rattle ) algorithm. But I only
> found some information about shake (verlet) algorithm. Mainly, which
> algorithms can be used in Amber 9/10 v. and how can I describe them in
> MD sanderinput files? Particularly, how can I describe velocity-verlet
> algorithm? Also Could you give me some information about using these
> integration algorithms with the right ensembles? For example I think that
> velocity-verlet algorithm should be used for NVE simulations.

Amber uses the velocity-verlet algorithm to propagate trajectories. Sander
and pmemd do not use rattle (which is implemented in NAB, by the way). I have
not seen arguments about why shake is not appropriate. Sander/pmemd will
conserve energy well in NVE simulations, for example.


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