[gmx-developers] Re:Accelerated MD

[Gleb Solomentsev]

Hi again,

First, Ran, thanks for the suggestion. I am familiar with this algorithm 
but its not quite what I want. Alex, thanks for the pointer.

So now, a refined version of the questions. The applied energy boost 
should be applied only to the solvent molecule and the contribution 
should be based on the dihedral and non-bonded potential terms.For me 
the most logical place to make the modification would be within the 
update routine (update.c) i.e. after all the energy terms have been 
evaluated, when updating system energies to tack on the boost energy to 
the solvent atoms.

Does anyone reason this to be problematic?

Thanks again for all help and suggestions,
Gleb


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> Today's Topics:
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>    1. Accelerated MD (Gleb Solomentsev)
>    2. Re: Accelerated MD (Ran Friedman)
>    3. Re: Accelerated MD (Alexander Herz)
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 27 Oct 2009 12:13:20 +0100
> From: Gleb Solomentsev <gleb.solomentsev at ucd.ie>
> Subject: [gmx-developers] Accelerated MD
> To: gmx-developers at gromacs.org
> Message-ID: <4AE6D5D0.8050806 at ucd.ie>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hello Developers,
>
> I am looking into implementing the Hamelberg Accelerated Molecular 
> Dynamics (J. Chem. Phys. *120*, 11919 (2004)) algorithm intro the latest 
> distribution of gromacs. Basically the algorithm modifies the potential 
> function, if the system energy is bellow a certain value. A boost energy 
> is applied to help the system escape energy wells when bellow an energy 
> threshold. When the system is above the threshold, the energies are 
> evaluated according to the original potential.
>
> I am not sure about the best way to structure the modification so 
> looking for suggestions. I have been fishing around the development 
> list, but not really seeing what I have in mind. Basically, I am trying 
> to find where the potential is evaluated for an interaction pair?
>
> Thanks for the help,
> Gleb
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 27 Oct 2009 12:35:04 +0100
> From: Ran Friedman <r.friedman at bioc.uzh.ch>
> Subject: Re: [gmx-developers] Accelerated MD
> To: Discussion list for GROMACS development
> 	<gmx-developers at gromacs.org>
> Message-ID: <4AE6DAE8.9020001 at bioc.uzh.ch>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi,
> Are you familiar with the flooding method of Grubmuller? It has been
> implemented in Gromacs and seems to be somewhat similar to the algorithm
> you describe.
> Ran
>
> Gleb Solomentsev wrote:
>   
>> Hello Developers,
>>
>> I am looking into implementing the Hamelberg Accelerated Molecular
>> Dynamics (J. Chem. Phys. *120*, 11919 (2004)) algorithm intro the
>> latest distribution of gromacs. Basically the algorithm modifies the
>> potential function, if the system energy is bellow a certain value. A
>> boost energy is applied to help the system escape energy wells when
>> bellow an energy threshold. When the system is above the threshold,
>> the energies are evaluated according to the original potential.
>>
>> I am not sure about the best way to structure the modification so
>> looking for suggestions. I have been fishing around the development
>> list, but not really seeing what I have in mind. Basically, I am
>> trying to find where the potential is evaluated for an interaction pair?
>>
>> Thanks for the help,
>> Gleb
>>
>>
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