Dear Sophia.
It looks to me that before trying to to replica exchange and pH changes,
you should familiarize yourself with just the regular constant pH runs.
Try looking at the manual and/or the constant pH files under the tests
directory in the amber directory.
Adrian
On 2/16/11 12:55 PM, Cheng-I Lee wrote:
> Dear Adrian and Jason,
>
> Thanks for the reply.
> What's difference between temperature space and pH-space? Could you please
> provide me some references?
>
> I'm interested in simulation of protein dynamics under specific pH values. I
> have AMBER 11 to work on and hope to work on it asap.
>
> Sophia
>
> On Tue, Feb 15, 2011 at 9:34 PM, Adrian Roitberg<roitberg.qtp.ufl.edu>wrote:
>
>> Hi Sophia
>>
>> If you want your replicas in temperature space, we can try to help you.
>> If you want your replicas to span pH-space, we just finished
>> implementing it in amber, but the code it still being debugged. Almost
>> surely we will release it for Amber 12.
>>
>> Best Regards
>> Adrian
>>
>>
>> On 2/15/11 2:30 PM, Cheng-I Lee wrote:
>>> Dear Amber users,
>>>
>>> I'm looking for a tutorial to run REMD at constant pH. Does anyone know
>> any
>>> website that shows REMD simulation at constant pH?
>>>
>>> Thanks a lot!
>>>
>>> Best wishes,
>>> Sophia
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>> --
>> Dr. Adrian E. Roitberg
>> Associate Professor
>> Quantum Theory Project, Department of Chemistry
>> University of Florida
>>
>> on Sabbatical in Barcelona until August 2011.
>> Email roitberg.ufl.edu
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
> _______________________________________________
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>
--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project, Department of Chemistry
University of Florida
on Sabbatical in Barcelona until August 2011.
Email roitberg.ufl.edu
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Received on Wed Feb 16 2011 - 06:30:06 PST
