restraints definition in amber is only use for freezing atoms angles and etc. I've try a lot but i can't create a wall (virtual or real).
Is there any example for this?
> From: jason.swails.gmail.com
> Date: Mon, 25 Jul 2011 21:17:20 -0400
> To: amber.ambermd.org
> Subject: Re: [AMBER] create walls
>
> Look for NMR restraints in the manual. "Flatwell" is the functional form of the NMR restraints.
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
> On Jul 25, 2011, at 7:07 AM, amir abbasi <amir-abbasi.hotmail.com> wrote:
>
> >
> > Thanks Jason, but I can't find any thing about "flatwell potential in amber" neither in amber users manual nor on web.
> > Is there any tutorial or example?
> > I want to produce virtual wall and a hole on it.
> >
> >> Date: Sat, 23 Jul 2011 12:22:03 -0400
> >> From: jason.swails.gmail.com
> >> To: amber.ambermd.org
> >> Subject: Re: [AMBER] create walls
> >>
> >> Try the NMR restraints (flatwell potential). See the corresponding chapter
> >> in the Amber manual.
> >>
> >> HTH,
> >> Jason
> >>
> >> On Sat, Jul 23, 2011 at 8:27 AM, amir abbasi <amir-abbasi.hotmail.com>wrote:
> >>
> >>>
> >>> Hi Dear Users,
> >>> I want to make a wall in my simulation and create a cavity (with an
> >>> arbitrary geometry) on it to force on a DNA to pull it from one side to
> >>> other.
> >>> any suggestions?
> >>>
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> >>>
> >>
> >>
> >>
> >> --
> >> Jason M. Swails
> >> Quantum Theory Project,
> >> University of Florida
> >> Ph.D. Candidate
> >> 352-392-4032
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Wed Jul 27 2011 - 07:00:02 PDT
