Dear All,
I agree with all that has been said.
The idea is to make it general, with enough comments and an API so
people can play with it later on.
The idea of making multi-pmemd first and then T-remd was to make sure we
could have a basic implementation without breaking things too much. Now
that we know it works, we move to the more complex picture.
Cheers
Adrian
On 4/7/11 5:21 PM, Jason Swails wrote:
> On Thu, Apr 7, 2011 at 6:35 AM, David A Case<case.biomaps.rutgers.edu>wrote:
>
>> On Wed, Apr 06, 2011, git repository hosting wrote:
>>>
>>> commit e6a48cd21926796aea3947f970b914530cad1b21
>>> Author: Jason Swails<jason.swails.gmail.com>
>>> Date: Wed Apr 6 17:44:38 2011 -0700
>>>
>>> Add a multi-sander like feature to pmemd (multipmemd)...
>>> Currently only T-REMD is implemented,
>>> but H-REMD and multi-D-REMD are upcoming.
>>
>> This sounds great! But I'm hoping that all these variants of REMD are in a
>> single place, with an eye towards a "general" REMD capability, that would
>> allow the user (perhaps only by modifying the code) to specify which
>> exchanges
>> should be tried, and what criterion should be used for acceptance. We want
>> to
>> facilitate exploration of new ideas, and not just hard-wire a series of
>> "xxx-REMD" options.
>>
>
> The multi-D-REMD should be this generalized functionality. For a
> generalized, N-dimensional replica exchange simulation, I can't see how more
> exchanges than just basic T-REMD (where only T exchanges because the rest of
> the hamiltonian is the same) and H-REMD (where the coordinates exchange and
> recalculate energies, so we have 4 energies total) could be needed to make
> it as general as possible (and then just allow for an arbitrary number of
> exchanging dimensions). I could imagine that people would want to change
> the acceptance criteria, but that's all centrally located in remd.fpp, so it
> shouldn't be too hard.
>
> My current plan is to parse an input file that maps all of the exchanges
> that are supposed to take place; an input file that could easily be
> script-generated or hand-generated for those that wish to fine-tune their
> REMD experience :)
>
> All the best,
> Jason
>
>
>> ...dac
>>
>>
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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 Fri Apr 08 2011 - 04:00:03 PDT
