Hi,
Thanks Tomas. I know that but there is a problem.Argon not defined in Amber. Not only Argon but also other inert gases.
I want that the wall interactions with my system is only van der waals interactions.
> Date: Wed, 27 Jul 2011 10:51:51 -0400
> From: steinbrt.rci.rutgers.edu
> To: amber.ambermd.org
> Subject: Re: [AMBER] create walls
>
> Hi,
>
> you could build a sheet out of inert atoms, say Argon, and freeze them
> into place with moderately strong restraints. If they are close together,
> this is effectively a wall even though it is not perfectly smooth. Even
> better, bond your wall atoms together into a mesh, then they wont repulse
> each other. From that, arbitrary wall shapes and locations can easily be
> scripted.
>
> Kind Regards,
>
> Thomas
>
> On Wed, July 27, 2011 9:36 am, amir abbasi wrote:
> >
> > 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?
> >> >>>
> >> >>> _______________________________________________
> >> >>> AMBER mailing list
> >> >>> AMBER.ambermd.org
> >> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>>
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Jason M. Swails
> >> >> Quantum Theory Project,
> >> >> University of Florida
> >> >> Ph.D. Candidate
> >> >> 352-392-4032
> >> >> _______________________________________________
> >> >> AMBER mailing list
> >> >> AMBER.ambermd.org
> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >> > _______________________________________________
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> >>
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>
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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Received on Thu Jul 28 2011 - 01:30:05 PDT
