Look at the generalized distance restraint NMR code (Amber10 or older).
This lets you define a RC composed of linear combinations of up to 4
distances.
See the chapter on NMR restraints (Chapter 6 in the Amber11 manual).
Alternatively, you can do it with the NCSU codes (see the adaptively biased
MD (ABMD) in chapter 4.7) of the Amber11 manual.
HTH,
Jason
On Fri, Apr 29, 2011 at 8:06 PM, iccy liu <hbliu92.hotmail.com> wrote:
>
> Dear AMBER users,
>
> I am trying to learn how to set up QM/MM simulations for reaction catalyzed
> by enzyme. I would performe umbrella sampling on my reaction coordiate (RC).
> Since my system involved in multiple bonds forming/bonds breaking, I wonder
> how to put a restraint on the differences of several key distanaces in my
> RC? AMBER can do simple distance constraint and angles, torsion angles as
> well. But what I need, for example, I have 4 key distances r1 r2 r3 r4, how
> to implement an harmonic restraint with a formular like
> k[(r2-r1)^2+(r4-r3)^2] to performe unbrella sampling in AMBER?
>
> Any help will be highly appreciated. Thanks!
>
> Iccy
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Apr 29 2011 - 13:30:03 PDT
