Re: wrong velocity in steered molecular dynamics

From: JC Gumbart (
Date: Sat Apr 07 2007 - 18:38:16 CDT

Check that the reference coordinates in your SMDfile match those
being loaded initially (either coordinates or binCoordinates in case
you are restarting from a previous simulation). My bet is that they
are very different.

If you are not starting from time 0, then they shouldn't match;
instead, the real coordinate should be approximately v*t away from
the reference.

On Apr 7, 2007, at 2:29 PM, Ana Celia Araujo Vila Verde wrote:

> Hi all,
> I'm running a SMD simulation, and I defined SMDVel as 0.00001
> (angstroms/timestep). The *log file confirms this velocity: "Info:
> However, during my simulation I find that the SMD atoms travel 38
> angstroms in 800 timesteps (0.0475 A/time-step or a whooping 5000
> meters/second...)
> Can anyone offer some insight as to what is going on?
> Thanks,
> Ana

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