Re: [AMBER] NVE GPU question

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 23 Jan 2015 10:37:55 -0500

On Fri, Jan 23, 2015 at 10:03 AM, Joseph Baker <bakerj.tcnj.edu> wrote:

> Hi all,
>
> Hector, thanks for the link. Our inputs are only different in that you have
> turned on SHAKE with a 1 fs timestep. I had not employed SHAKE with the 1
> fs timestep simulations, as I thought ntc=ntf=2 is typically only required
> when going to a 2 fs timestep and/or when TIP3P water is included in the
> simulation.
>

‚ÄčThis depends strongly on the frequencies of the fastest motions (which is
really just a reflection of how big the forces become). The stronger the
forces (higher the frequencies of some motions), the shorter time step that
is needed.

For typical protein simulations, 0.002 with SHAKE and 0.001 without are
*typically* sufficient. It wouldn't surprise me if the IL forces are too
high for those time steps to conserve energy as well. But I *would* be
surprised if 0.0001 fs was still too long even without SHAKE (I thought I
remembered you mentioning that you tried that timestep...).

This is still all conjecture until the range in which the forces in the IL
and protein simulations occur is established, though.

(I also think that a CPU simulation would be useful to eliminate a quirk in
the GPU code as a culprit).

All the best,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Jan 23 2015 - 08:00:03 PST
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