Elisa,
Look at the Center of Mass restraints in the manual.
Also, if you want distance and angle PMF, you would need at least a 2-D
umbrella sampling scheme.
adrian
On 1/15/13 9:12 AM, Elisa Frezza wrote:
> Dear All,
>
> I am doing Umbrella Sampling on a pair of dodecamer and I would like to
> obtain the PMF as a function of the relative distance and orientation.
> I have noticed that I have to use a lot of restrains.
> My question is:
> is it right to put the restraint for each bond? Is it right to obtain the
> PMF?
>
> My restraint files is like this:
>
>
> #DNA
> #dna
> &rst
> iat=62,820
> r1=0.0000E+00,r2=28.0000,r3=28.0000,r4=56.000,rk2=5,rk3=5,ir6=0,
> &end
> &rst
> iat=92,850
> r1=0.0000E+00,r2=28.0000,r3=28.0000,r4=56.000,rk2=5,rk3=5,ir6=0,
> &end
> &rst
> iat=125,883
> r1=0.0000E+00,r2=28.0000,r3=28.0000,r4=56.000,rk2=5,rk3=5,ir6=0,
> &end
>
> ......
>
> thank you in advance
>
> Elisa
>
--
Dr. Adrian E. Roitberg
Professor
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
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Received on Tue Jan 15 2013 - 06:30:03 PST
