Dear Adrian
thank you for prompt reply. I went through jar and I think I still miss a
clear picture. for example, in the A26 tutorial, the velocity is 100 Å/ns
and 10 Å/ns but you can not see these velocities in the namelist. And
if one wants to choose optimum spring constant and velocity.
Thank you in advance,
On Sun, Jul 24, 2016 at 7:35 PM, Adrian Roitberg <roitberg.ufl.edu> wrote:
> Look at the manual flag "jar" and also look at some tests under jar in
> the test dir for the amber installation. That should get you some ideas.
>
> adrian
>
>
>
> On 7/24/16 6:25 PM, Ibrahim Said wrote:
> > Dear Amber Users
> > I am planning to study the mechanical properties of a protein with
> steered
> > molecular simulation but unfortunately I can not find a protocol for
> amber.
> > Also, I can not find the position of the constant velocity in the
> namelist.
> >
> > Please, any help is appreciated.
> >
> > thank you
> > _______________________________________________
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>
> --
> Dr. Adrian E. Roitberg
> University of Florida Research Foundation Professor.
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
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>
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Received on Sun Jul 24 2016 - 13:30:02 PDT
