Re: [AMBER] Energy and Coordinate Outputs

From: David A. Case <>
Date: Wed, 14 Mar 2012 17:15:58 -0400

On Tue, Mar 13, 2012, Jason Swails wrote:
> The 1-time-step-off is expected. The workflow in the MD routine is this:
> 1. calculate energies and forces on the current structure
> 2. propagate dynamics
> 3. If printing, print the structure and the energies (Do _not_ recalculate
> the energy)

Just to expand a bit on Jason's post: the reason to delay printing until after
the coordinate update step was that, in the leap-frog method, the velocity
estimate at time t depends on knowing velocities at t-1/2h and t+1/2h. Since
we want to print an estimate of the kinetic energy along with the potential
energy, such a delay makes some sense.

The whole thing was decided (arguably sub-optimally) back in the early 80's.
Changing things would break backwards compatibility in a way that has been
considered too serious to carry out.


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Received on Wed Mar 14 2012 - 14:30:02 PDT
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