Re: [AMBER] Replica Exchange

From: Adrian Roitberg <roitberg.ufl.edu>
Date: Wed, 14 Mar 2012 11:40:46 -0400

Just to make sure we are all in the same page here.

You can (and should!) equilibrate in NPT before starting the NVT REMD.

However, ALL replicas MUST have the same box size! (this is true for
Amber's implementation).

What this means is that you SHOULD NOT do NPT for each replica
separately, followed by NVT remd.


adrian


On 3/14/12 11:34 AM, Logan Ahlstrom wrote:
> For explicit solvent REMD, equilibration in the NPT ensemble in can be
> performed for a few hundred picoseconds at 300 K before running REMD in NVT.
>
> Paschek, D., H. Nymeyer, and A. E. Garcia. 2007. Replica exchange
> simulation of reversible folding/unfolding of the Trp-cage miniprotein in
> explicit solvent: on the structure and possible role of internal water. J.
> Struct. Biol. 157:524533.
>
> Sanbonmatsu, K. Y., and A. E. Garcia. 2002. Structure of Met-enkeph- alin
> in explicit aqueous solution using replica exchange molecular dynamics.
> Proteins. 46:225234.
> Ahlstrom, L. S. and Miyashita, O. 2011. Molecular Simulation Uncovers the
> Conformational Space of the lambda Cro Dimer in Solution. Biophys. J.
> 101:2516-2524.
>
>
> On Wed, Mar 14, 2012 at 8:29 AM, Carlos Simmerling<
> carlos.simmerling.gmail.com> wrote:
>
>> replica exchange at NPT is not currently supported in Amber. This is
>> tricky, since in principle the system would boil at the high T normally
>> used for REMD. Look at work by Garcia and others to see how this can be
>> handled.
>>
>> On Wed, Mar 14, 2012 at 11:22 AM, Rajendra Sharma<rajenbiotech.gmail.com
>>> wrote:
>>
>>> Dear All,
>>>
>>> In replica exchange simulations, is NPT simulations are possible for
>>> equilibration followed by NVT for the production run?
>>>
>>> Sincerely,
>>>
>>> Rajendra Sharma
>>>
>>> On Wed, Mar 14, 2012 at 2:04 AM, Dmitry Mukha<dvmukha.gmail.com> wrote:
>>>
>>>> Hi, Rajendra,
>>>>
>>>> try 'remd temperature' query in g**gle
>>>>
>>>> 2012/3/13 Rajendra Sharma<rajenbiotech.gmail.com>
>>>>
>>>>> Dear All,
>>>>>
>>>>> I have to perform explicit solvent replica exchange simulations on a
>>>> small
>>>>> peptide. I am not sure how to decide the number of replicas and
>>>>> temperatures. It would be of great help ifi get a tutorial or
>>>> publication
>>>>> to perform the simulations.
>>>>>
>>>>> Sincerely,
>>>>>
>>>>> Rajendra
>>>>>
>>>>> --
>>>>> Rajendra Sharma
>>>>> Junior Research Fellow,
>>>>> Computational Biophysics,
>>>>> *National Center for Biological Sciences,*
>>>>> (Tata institute of Fundamental Research)
>>>>> India.
>>>>> Mobile No. +91-9950675288
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Sincerely,
>>>> Dmitry Mukha
>>>> Institute of Bioorganic Chemistry, NAS, Minsk, Belarus
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>>
>>>
>>> --
>>> Rajendra Sharma
>>> Junior Research Fellow,
>>> Computational Biophysics,
>>> *National Center for Biological Sciences,*
>>> (Tata institute of Fundamental Research)
>>> India.
>>> Mobile No. +91-9950675288
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>

-- 
                            Dr. Adrian E. Roitberg
                                  Professor
                Quantum Theory Project, Department of Chemistry
                            University of Florida
                              roitberg.ufl.edu
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Received on Wed Mar 14 2012 - 09:00:04 PDT
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