Re: [AMBER] fix CM

From: Jason Swails <>
Date: Fri, 30 Jul 2010 16:14:28 -0400


If you are looking for a PMF along this coordinate, you can ALMOST do this
with NMR restraints via MSMD simulations and Jarzynski's equation or
umbrella sampling with WHAM to remove the bias. See in particular setting
iat values to < 0. This will do exactly what you describe, but it will use
coordinate-averaged positions, which is not a COM unless all atoms are the
same. It would probably be pretty trivial to hack the code and use
mass-weighted coordinates rather than equally-weighted coordinates, but
maybe average position (rather than COM) will be good enough for what you're
trying to do?

The relevant part of the Amber11 manual that describes this is page 172.
This functionality exists for Amber10 also, but not older versions
(according to the manual).

Hope this helps,

On Fri, Jul 30, 2010 at 3:43 PM, riya david <> wrote:

> Dear Amber
> I am a new user to amber . I would like to know how one can fix
> a center of mass for two groups of atoms in a DNA and to do simulation by
> varying the distance between them
> the labeling and masking are difficult to me .
> thanking you
> riya
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Fri Jul 30 2010 - 13:30:03 PDT
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