Dear Aron,
thank you very much for your answer. I am using PMEMD GPU in AMBER12, and I
try to use COM restraint but it fails.
It is quite difficult to explain you without a figure what I am doing. If
you want, I can write in your private email and I am trying to explain you
better.
Thank you in advance
Elisa
2013/1/15 Aron Broom <broomsday.gmail.com>
> 1) I believe you can indeed do a COM restraint (I assume you mean the
> distance between multiple atoms center of mass?), it just requires defining
> groups, it should all be in the manual under the NMR refinement section.
>
> 2) For umbrella sampling, you can define say an angular restraint (or
> several) to hold things in the orientation you want and then do the
> umbrella sampling along just a distance. This will work and if not
> uncommon, but you just have to be aware that the PMF you are getting is for
> that particular movement only. If you have good reason to think that is
> the most energetically relevant movement (i.e. lowest free energy path)
> then it is a fair assumption to make.
>
> ~Aron
>
> On Tue, Jan 15, 2013 at 7:11 AM, Elisa Frezza <elisa.frezza.gmail.com
> >wrote:
>
> > Have you any suggestions?
> >
> >
> > 2013/1/15 Elisa Frezza <elisa.frezza.gmail.com>
> >
> > > 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
> > >>
> > >>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >
> > >
> > >
> > > --
> > > 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
> > >
> > >
> > >
> >
> >
> > --
> > 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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 - 07:30:05 PST
