AMBER Archive (2007)

Subject: Re: AMBER: constant-pH MD with replica exchange

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Thu Oct 11 2007 - 13:55:18 CDT

Carlos Simmerling wrote:
> why doesn't it work standard?
> is there something other than energy needed for exchange
> is it because the reps might have different protonation?
exactly !

as I wrote: "Since the protonation state of a residue can be different
in different temperatures, one needs to be very careful with the
exchange equations, but it all works out ok." ;-)

.

>
> On 10/11/07, Adrian Roitberg <roitberg_at_qtp.ufl.edu> wrote:
>> Maciek,
>>
>> We have been working on this, and will be sending a paper out next week
>> for publication.
>>
>> Basically, Amber 9 cannot do this as distributed, but we hope to have
>> the code in for the next release.
>>
>> Doing constant pH and replica exchange in pH space turns out to be
>> inefficient in terms of sampling conformational space.
>>
>> So, what we do is to run constant pH MD doing REMD at different
>> temperatures. Since the protonation state of a residue can be different
>> in different temperatures, one needs to be very careful with the
>> exchange equations, but it all works out ok.
>>
>> Adrian
>>
>>
>> Maciej Dlugosz wrote:
>>> Dear Amber developers/users:
>>>
>>> Is this possible to run constant-pH MD with
>>> replica exchange?
>>> Has anyone tried?
>>>
>>> Thanks,
>>>
>>> maciek
>>>
>>>
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>> --
>> Dr. Adrian E. Roitberg
>> Associate Professor
>> Quantum Theory Project and Department of Chemistry
>>
>> University of Florida PHONE 352 392-6972
>> P.O. Box 118435 FAX 352 392-8722
>> Gainesville, FL 32611-8435 Email adrian_at_qtp.ufl.edu
>> ============================================================================
>>
>> To announce that there must be no criticism of the president,
>> or that we are to stand by the president right or wrong,
>> is not only unpatriotic and servile, but is morally treasonable
>> to the American public."
>> -- Theodore Roosevelt
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>
> 

-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu
============================================================================

To announce that there must be no criticism of the president,
or that we are to stand by the president right or wrong,
is not only unpatriotic and servile, but is morally treasonable
to the American public."
   --  Theodore Roosevelt
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