We are in the process of writing a bugfix for amber 9.0 on this and will
be sent to the archives when ready, hopefully this week.
Adrian
Alik Widge wrote:
> As a followup, mainly so this gets archived:
>
> I've talked to Dr. Adrian Roitberg, who's listed in the manual as one of
> the contacts for the SMD code, and he has been able to reproduce my
> problem. It turns out to be the inherent behavior of the NMR/restraints
> code, which underlies the SMD implementation.
>
> The easy way to prevent the issue is that instead of following the example
> in the manual and writing, e.g.,
>
> &rst iat=485,134, r2=15.0,r2a=20.0, rk2=5000.0 /
>
> one must also set the "rk2a" variable to the same value as "rk2":
>
> &rst iat=485,134, r2=15.0,r2a=20.0, rk2=5000.0, rk2a=5000.0 /
>
> My thanks to Dr. Roitberg for iterating on this with me over email and
> helping me get my project back on track!
>
> Alik
>
>
>
> On Mon, 24 Jul 2006, Alik Widge wrote:
>
>> 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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--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project and Department of Chemistry
University of Florida PHONE 352 392-6972
P.O. Box 118435 FAX 352 392-8722
Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
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Received on Wed Aug 02 2006 - 06:07:11 PDT
