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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>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Wed Jul 27 2011 - 08:00:03 PDT
