On Fri, Apr 29, 2011, iccy liu wrote:
>
> 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?
Note that this is just the sum of two restraints, one on r2-r1 and another
on r4-r3. It's likely that a two-dimensions PMF for both of these might
be more helpful than a combo in which both have the same force constant.
However, as far as I know, Amber restraints don't include the difference of
two distances. This is such a widely used type of progress variable that I
hope some developer will think about implementing it. [It might be that the
ncsu code already does this, but it didn't look like that on a quick glance.]
...regards...dac
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Received on Wed May 04 2011 - 07:00:03 PDT
