Hi
First, let me point out that:
k[(r2-r1)^2+(r4-r3)^2]
is not a restrain, as shown by the fact that there is nothing to
restrained to !
You require at least a value of a restraint distance.
A potentially correct writing (but I do not know if the writer means
this!) is
k[(r2-r1 - r^0_21)^2+(r4-r3 -r^0_34)^2]
This would restrain EACH of the two differences to a particular value of
the difference.
If this is what the original writer wants, then I agree with Dave, you
are in fact doing a 2D umbrella, since you have two coordinates.
Now, I disagree with Dave in that difference of distances IS already in
the amber code.
Things like this (please look at the manual, page 177 for amber11):
&rst
iat=5320,9630,5320,5321, r1=-10, r2=$x , r3=$x , r4=20 , rk2=$ku,
rk3=$ku,rstwt=-1.0,1.0,
&end
&rst
iat=9811,921,9809,9630, r1=-10, r2=$lengthstart,r3=$lengthstart
,r4=20, rk2=$ku, rk3=$ku,rstwt=1.0,1.0,
&end
will do a 2-D umbrella, where the first coordinate is defined as R1 - R2
and the second coordinate is defined as
R3 + R4
The manual mentions:
rstwt(1)→rstwt(4) New as of Amber 10 (sander only), users may now define
a single restraint that is a function of multiple distance restraints,
called a "generalized distance co- ordinate" restraint. The energy of
such a restraint has the following form:
U = k(w1|r1 −r2|+w2|r3 −r4|+w3|r5 −r6|+w4|r7 −r8|−r0)2 where the weights
wnare given in rstwt(1)..rstwt(4) and the positions rn are the positions
of the atoms in iat(1)..iat(8).
Cheers
Adrian
On 5/4/11 3:33 PM, David A. Case wrote:
> 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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>
--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project, Department of Chemistry
University of Florida
on Sabbatical in Barcelona until August 2011.
Email roitberg.ufl.edu
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Received on Wed May 04 2011 - 07:00:04 PDT
