[gmx-developers] modifying replica exchange to allow Hamiltonian exchanges

[Shirts, Michael (mrs5pt)]

>  Thank you for the quick response.
> I am sorry but I am not sure to correct understand
> "[..]is not correct unless lambda is a linear coupling parameter."

No, this has to do with how the Hamiltonian depends on lambda.  Linear means
that if H_A and H_B are the end states, then H(lambda) = (1-lambda) H(A) +
lambda H(B).  Softcore VDW terms are not linear.

> It means that, delta lambda must be equal for all replicas?
> Can you provide an estimation of the next release date?

That is something that I'm not in charge of deciding!

Best,
~~~~~~~~~~~~
Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
(434)-243-1821


> From: Luca Bellucci <lcbllcc at gmail.com>
> Date: Sat, 26 Feb 2011 06:21:30 -0500
> To: "michael.shirts at virginia.edu" <michael.shirts at virginia.edu>, Discussion
> list for GROMACS development <gmx-developers at gromacs.org>
> Subject: Re: [gmx-developers] modifying replica exchange to allow Hamiltonian
> exchanges
> 
>  Thank you for the quick response.
> I am sorry but I am not sure to correct understand
> "[..]is not correct unless lambda is a linear coupling parameter."
> It means that, delta lambda must be equal for all replicas?
> Can you provide an estimation of the next release date?
> Best,
> Luca
> 
>>> I performed Hamiltonian replica exchange with gromacs 4.5.3
>>> using the FEP module and the capabilty of repl_ex.c routine
>>> to recognize  lambda values as replica exchange quantities.
>>> I run some tests and they seems to work fine, however, I do not find any
>>> documentation about it.
>> 
>> Hamiltonian replica exchange in the 4.5.3 release version is not correct
>> unless lambda is a linear coupling parameter.  A fully general version is
>> being tested right now, and will likely be part of the next release.
>> 
>> Best,
>> ~~~~~~~~~~~~
>> Michael Shirts
>> Assistant Professor
>> Department of Chemical Engineering
>> University of Virginia
>> michael.shirts at virginia.edu
>> (434)-243-1821
>> 
>>> From: Luca Bellucci <lcbllcc at gmail.com>
>>> Date: Sat, 26 Feb 2011 05:48:56 -0500
>>> To: "michael.shirts at virginia.edu" <michael.shirts at virginia.edu>,
>>> Discussion list for GROMACS development <gmx-developers at gromacs.org>
>>> Subject: Re: [gmx-developers] modifying replica exchange to allow
>>> Hamiltonian exchanges
>>> 
>>> Dear all,
>>> I performed Hamiltonian replica exchange with gromacs 4.5.3
>>> using the FEP module and the capabilty of repl_ex.c routine
>>> to recognize  lambda values as replica exchange quantities.
>>> I run some tests and they seems to work fine, however, I do not find any
>>> documentation about it.
>>> 
>>> Since it seems that this capability is under development, I have
>>> some "uncertainty" in using it and I am not completely sure of
>>> its "reliability".
>>> I would like to take this opportunity to submit some questions:
>>> Can I use this capability for production run?
>>> Where can I find more info?
>>> 
>>> Thank you
>>> Luca
>>> 
>>>> This has been added in a branch, and the plan is for this functionality
>>>> to be included in the next Gromacs release.  We can discuss whether it
>>>> would be useful for specific individual to use this test code right now,
>>>> or whether it may be best to wait until there has been a chance for it
>>>> to be tested more.  There area a number of other free energy changes
>>>> included in this code as well.
> 
>