Hi
Let me add my 2 cents here.
You can look at papers by the PLUMED people, or some implementation
inside NAMD for this.
Basically, what they do is create a continuous function of distance
between two groups, which goes from zero when distance > distance_0 and
to one when distance < distance_0 with some simple polynomial
extrapolation, so the change is smooth.
Since you now have a differentiable form, you can do umbrella, FEP, etc.
Amber itself does not have this, but the PLUMED plugin to amber does.
Disclaimer, I have seen this advertised but never used it, so caveat emptor.
In terms of how wise that is, I agree with Carlos that I do not think it
wise at all...
Imagine you want an umbrella of 4 native contacts, out of a total of 10.
Once you find a particular set of 4 that satisfies the umbrella window,
it would be almost impossible to unmake that and sample a DIFFERENT set
of 4 contacts, since you would have to break at least some of the
original ones.
I also believe that things like native contacts, etc are better used as
analysis objects, AFTER your simulations is done, but not as simulation
drivers.
adrian
On 5/5/14 7:25 PM, Carlos Simmerling wrote:
> I can imagine creating a pmf from a histogram of population vs Q for
> converged ensembles. What's much harder to imagine is implementing Q as a
> coordinate for something like umbrella sampling. On top of being
> discontinuous, it would be counterproductive since it would strongly hinder
> the sampling orthogonal to Q.
> On May 5, 2014 6:50 PM, "Nihal Korkmaz" <enihalkorkmaz.gmail.com> wrote:
>
>> Dear Amber Community,
>>
>> I am aiming to implement Q (fraction or number of native contacts) as a
>> reaction coordinate for PMF just like we conventionally use distance or
>> angle restraints.
>>
>> If there is anyone tackled/attempted this issue before, I appreciate any
>> suggestions.
>>
>> Best,
>> Nihal
>>
>> --
>> E. Nihal Korkmaz
>> UW-Madison, Biophysics Program
>> Qiang Cui Lab
>> Phone: 608-265-3644
>> E-mail: korkmaz.wisc.edu
>>
>>
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>>
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--
Dr. Adrian E. Roitberg
Colonel Allan R. and Margaret G. Crow Term Professor.
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Tue May 06 2014 - 07:30:03 PDT
