AMBER Archive (2007)

Subject: Re: AMBER: question about ntx=5

From: Wei Chen (cwbluesky_at_gmail.com)
Date: Sun Nov 25 2007 - 19:21:52 CST

Dr. Case,

Thank you for reply. 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?

Wei Chen

On 11/25/07, David A. Case <case_at_scripps.edu> wrote:
>
> On Sun, Nov 25, 2007, Wei Chen wrote:
> >
> > I restart my simulation with ntx=5, reading in coordinates and
> velocities.
> > This is a non-periodic simulation, ntb=0. I also set nscm=0 because I do
> not
> > want to remove the velocity of center of mass. But I found that the
> velocity
> > of center of mass was removed at first restart step. How can I avoid
> this?
>
> As I read the code, it should not be possible for the center of mass
> motion to
> be removed if nscm=0. Can you post a short md output file that
> illustrates
> the behavior you are seeing?
>
> ...thx...dac
>
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