Re: [AMBER] create walls

From: Jason Swails <jason.swails.gmail.com>
Date: Mon, 25 Jul 2011 21:17:20 -0400

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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Received on Mon Jul 25 2011 - 18:30:03 PDT