From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sun Apr 08 2007 - 14:38:15 CDT
The SMD code in NAMD calculates the reference position using the formula x =
x0 + v*t (in one dimension) where x0 is the coordinate in SMDfile. This
makes sense for restarting SMD simulations, so you don't have to constantly
So in your case, your reference position is some distance away from the
position in SMDfile AND the real position of the COM of the selected atoms.
So there is a very large force on them trying to pull them to the reference
Why do the coordinates in the *coor file match those in SMDfile? Were you
not doing SMD initially?
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Ana Celia Araujo Vila Verde
Sent: Sunday, April 08, 2007 1:56 PM
Subject: RE: namd-l: wrong velocity in steered molecular dynamics
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?
From: JC Gumbart [mailto:gumbart_at_ks.uiuc.edu]
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
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:
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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