See below.
On May 4, 2011, at 8:57 AM, Adrian Roitberg wrote:
> 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
The NCSU code does this as well. Volodymyr Babin coded this at my request as a
patch for Amber10, and it is in Amber11 as released (at least that was the plan).
It is called "Linear Combination of Distances", LCOD, in the documentation.
Bud Dodson
--
M. L. Dodson
Business email: activesitedynamics-at-gmail-dot-com
Personal email: mldodson-at-comcast-dot-net
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Phone: eight_three_two-five_63-386_one
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Received on Wed May 04 2011 - 07:30:02 PDT
