it's better to apply strong positional restraints (see the ntr option in the
manual) unless you really need the coordinates not to change at all. with
restraints and a force constant of 10 to 100, the motion will be very small.
On Tue, Jun 16, 2009 at 9:11 AM, Yunjie Zhao <yjzhao.wh.gmail.com> wrote:
> Dear Amber users,
>
> Using Amber 9, I am trying to do molecular simulations with GB implicit
> solvent model. The PDB file has 28 residues. I want to fix the local
> structure (such as 15 to 23) as a rigid body when I do the molecular
> simulations.
>
> I do not know how to do this, can someone help me to figure it out? Any
> response will be appreciated.
>
> Thanks!
> Yunjie Zhao
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>
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Received on Mon Jul 06 2009 - 09:46:24 PDT
