RE: wrong velocity in steered molecular dynamics

From: Ana Celia Araujo Vila Verde (
Date: Sun Apr 08 2007 - 13:56:29 CDT

Hi JC,
Thanks for the suggestion. I checked and the reference coordinates in my SMDfile exactly match the ones in the *coor file that I use for the restart.
I'm not starting from time zero, but I can't understand exactly what you mean when you say that the coordinates should not match in this case. Is there a reference I can read to understand what you mean?
Thanks again,


From: JC Gumbart []
Sent: Sat 4/7/2007 7:38 PM
To: Ana Celia Araujo Vila Verde
Subject: Re: namd-l: wrong velocity in steered molecular dynamics

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: SMD VELOCITY 1e-05 ANGSTROM/TIMESTEP"
        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?

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