AMBER Archive (2006)

Subject: AMBER: Confusion re AMBER SMD output

From: Alik Widge (
Date: Mon Jul 24 2006 - 15:31:34 CDT

Hello again,

I have been exploring the application of the AMBER9 steered MD code to my
system, and have discovered something that I do not quite understand.
According to the manual, when I specify that the SMD history should be
dumped to a file, I should get four columns:

x0 x_actual force work

If I further understand this correctly, the "force" column should tell me
the current value of the restraint force on the atom(s) being steered,
according to the usual restraint force F = K*(x - x_0)**2 . However, that
is not consistent with the values I am observing in the output. For
instance, if I run the test given under /test/jar , the first few lines of
the output are:

    15.00000 15.12396 -1239.55482 0.00000
    15.00500 14.75768 2470.68119 3.07782
    15.01000 15.13490 -1246.46571 6.13835
    15.01500 15.15041 -1350.03026 -0.35289
    15.02000 14.77085 2481.56731 2.47596
    15.02500 15.12423 -987.34073 6.21152
    15.03000 15.18296 -1520.41603 -0.05787

I am fairly certain this output is correct, because it's similar to what
the test's "save" file contains, and it also matches the example in the
AMBER9 manual. However, the "force" column is clearly not K*(x-x0)**2. In
this part of the file, the relation is more like 2*K*(x0-x).

What's even more strange is that, towards the end of the run, the forces
appear to decay to zero even though there is still substantial error
between the commanded and actual positions. Again looking at the /test/jar
file, I find:

    19.96500 19.90832 3.96732 66.99162
    19.97000 19.89329 4.60255 67.01305
    19.97500 19.87926 4.78696 67.03652
    19.98000 19.86629 4.54839 67.05986
    19.98500 19.85980 3.75589 67.08062
    19.99000 19.86077 2.58457 67.09647
    19.99500 19.86732 1.27678 67.10612

Just looking at the last line, with a force constant of 5000 kcal/mol
(which is what's specified in the dist.RST file), the force should be in
the hundreds. In actuality, the force is 10*(x0-x).

I can precisely compute the forces in the entire file with the equation:

        F = 10*(# steps remaining)*(x0 - x)

Could some wiser person please explain to me what I am seeing? Does the
dist_vs_t file simply not contain the information I think it does? Or, if
I am right, why are the forces being computed in this very strange way?
Are the forces in dist_vs_t the actual forces that are being applied to
the steered atoms?

Alik Widge
The Robotics Institute
Carnegie Mellon University

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