Re: [AMBER] umbrella sampling

From: Elisa Frezza <elisa.frezza.gmail.com>
Date: Mon, 15 Oct 2012 14:13:28 +0200

Dear Jason,

thank you very much. Hence, if I would like to do US for dihedral angle, I
have to choose 4 atoms, havent't I?

thanks

Elisa

2012/10/15 Jason Swails <jason.swails.gmail.com>

> On Mon, Oct 15, 2012 at 3:32 AM, Elisa Frezza <elisa.frezza.gmail.com
> >wrote:
>
> > Dear All,
> >
> > I would like to do umbrella sampling and to use as restraint angle the
> > angle between two duplex of DNA.
> > How can I do this? Can I define 4 center of mass and make the restraint
> > using them?
> >
>
> 4 coordinates are for dihedral restraints. Angle restraints use 3. If you
> want to use COM restraints for angles or dihedrals, you can do this with
> sander (only).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> 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
UniversitÓ 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
Received on Mon Oct 15 2012 - 05:30:04 PDT
Custom Search