Dear Adrian,
thank you very much for your answer. I am using AMBER12 and I am not sure
that I can use COM restraint.
At the same time, if I use only a distance restraint, my molecules start to
rotate and they are not parallel each other.
In conclusion, my question is: Can I put a lot of restraints and then
consider only a distance between two atoms or is it not right?
Elisa
2013/1/15 Adrian Roitberg <roitberg.ufl.edu>
> 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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>
--
Elisa Frezza
Ph.D. Student in Materials Science and Engineering
Dipartimento di Scienze Chimiche
Università di Padova
via Marzolo, 1
35131 Padova - Italy
Phone: +39 049 827 5149
Skype: elisa.frezza
Emai: elisa.frezza.gmail.com
elisa.frezza.studenti.unipd.it
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Received on Tue Jan 15 2013 - 06:30:04 PST
