AMBER Archive (2006)

Subject: Re: AMBER: md and implicit solvation

From: David A. Case (
Date: Tue Oct 24 2006 - 20:47:18 CDT

On Wed, Oct 25, 2006, Jardas sucuriba wrote:

> My system is SuSE Linux 9.2 (x86-64) and I used two nodes.
> What I thought strange is that running the 50 ps in explicit solvation
> (using the same protein and 2 nodes) takes only half a day. Is it normal
> this difference between the two types of MD? As I cannot use more than two
> nodes is there other way to "speed up" the simulation?

This is not unprecedented: the "win" you get with PME in explicit solvent can
more than make up for having the extra coordinates of all the waters. This is
especially true for very large systems (and yours counts as "large" here).
There is not yet any equivalent speed-up for long-range interactions in GB
(which is why you have to use large cutoffs, as you are doing.)


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