Re: [AMBER] weird output of SMD simulation combined with Constant pH

From: Jason Swails <>
Date: Mon, 7 Dec 2015 21:55:31 -0500

On Mon, Dec 7, 2015 at 8:34 PM, Gustavo Seabra <>

> I see…
> From looking at the plot, I was under the impression that the SMD code
> worked well, and the problem appeared only in the analysis from CPPTRAJ.
> Isn’t that true? Or what “supposed” and “output” actually mean?

​The way I read it was the black line is what you get if you analyze the
trajectory, the blue line is what you get if you look at the jar.out file
(which is a distance dump), and the red line is the target position
assuming a constant velocity pulling. Clearly the trajectory is outpacing
the distance dump, which indicates to me that the steering is "active"
during the relaxation dynamics. And the pulling code thinks the simulation
is finished before it really is.​

I could be wrong, but I wrote the explicit solvent constant pH code (and am
generally familiar with a lot of the rest) and this is my best guess. I
haven't run the necessary tests to confirm, but this explanation is
consistent with the observed behavior here and seems likely.

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Dec 07 2015 - 19:00:02 PST
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