AMBER Archive (2007)

Subject: Re: AMBER: question about ntx=5

From: David A. Case (case_at_scripps.edu)
Date: Tue Nov 27 2007 - 10:49:33 CST

On Sun, Nov 25, 2007, Wei Chen wrote:
>
> Actually, I am just suspecting the velocity of center
> of mass was removed. I am running a steered MD with langevin dynamics on.
> When I restart the simulation at certain point, I found the loading force
> suddenly dropped and then increased gradually again. Because the friction
> force is proportional to the speed, I suspect that the sudden drop of force
> is due to the change of the velocity of center of mass. Where can I find the
> velocity of center of mass in md output?

If you are indeed remove COM velocity, an informative message with the phrase
"check COM velocity" will appear in the output.

It sounds to me like something else is going on in your situation, however.

...dac

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