Hi Ibrahim,
As you stated in your previous email, the velocity is not an explicit
namelist variable but it can be inferred through the md inputs. The
velocity can be calculated by the distance-pulled / nstlim*dt (be careful
with the units).
Choosing an optimum value for the spring constant is not always clear in my
experience, it takes some trial and error. I encourage you to consult the
literature and employ different values to evaluate how the results vary.
hope that helps,
Dwight
On Sun, Jul 24, 2016 at 4:08 PM, Ibrahim Said <saidibrahim569.gmail.com>
wrote:
> 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
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > --
> > Dr. Adrian E. Roitberg
> > University of Florida Research Foundation Professor.
> > Department of Chemistry
> > University of Florida
> > roitberg.ufl.edu
> > 352-392-6972
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
--
T. Dwight McGee Jr.
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Sun Jul 24 2016 - 15:00:02 PDT
