[gmx-developers] re: Energy and Foreign Lambdas and Hamiltonian Replica

[Erik Lindahl]

Berk is right - I haven't bothered with replica exchange stuff yet.

Cheers,

Erik

On Feb 15, 2008, at 5:12 PM, Berk Hess wrote:

> Hi,
>
> That code is probably only for efficiently determining the potential  
> energy at a different
> lambda than that of the actual run. This is useful for determining  
> the exchange probability.
>
> But one could also just use the average dH/dlambda of the two  
> replicas multiplied
> by delta lambda. This is very easy to code.
> I was actually thinking of doing this, but I currently don't need it  
> myself.
> To make it more efficient, you probably also want to be able to add  
> a biasing potential
> which is a function of lambda.
>
> Berk.
>
>
> servaas michielssens wrote:
>
>> Thanks, for your fast reply and for the code.
>> I had a look in the code but I can't find the swapping probability  
>> for hamiltonian replica exchange. I expected this in repl_ex.c but  
>> I can't find anything like it. I could not locate another function  
>> in md.c or mdrun.c to do the hamiltonion replica exchange. Could  
>> you help me al little further here were to look?
>>   thanks!
>> servaas
>>
>> Date: Fri, 15 Feb 2008 11:56:16 +0100
>>
>> Hi,
>>
>> My own server is unfortunately down since it was hacked last week  
>> and we were anyway about to move from Joomla to Dekiwiki, but I've  
>> uploaded a copy to the ftp site. Have a look in
>>
>> ftp://ftp.gromacs.org/pub/tmp/multilambda/
>>
>> Not sure if it's useful for your stuff, and since I haven't gotten  
>> much feedback for it yet you shouldn't use it for production  
>> purposes without significant testing. You've been warned, have  
>> fun ;-)
>>
>> Cheers,
>>
>> ERik
>>
>> Have a look at the
>> On Feb 15, 2008, at 11:22 AM, servaas michielssens wrote:
>>
>> > Hi,
>> >
>> > I am planning to do a hamiltonian replica exchange simulation and  
>> I > came acros this message. I am wondering what the status of this  
>> work > is and if it is possible to obtain a copy of the code to do  
>> > hamiltonain replica exchange. Or if not some suggestion on the  
>> best > way to implement the extra energy evalution with a topoly on  
>> > anonther node.
>> >
>> >
>> > kind regards,
>> >
>> > servaas
>> >
>> >
>> > Hi David,
>> >
>> > On Nov 2, 2007, at 5:19 PM, David Mobley wrote:
>> > >
>> > >> There is nearly no difference between the two as far as the  
>> replica
>> > >> stuff is concerned.
>> > >> It will be more work to (correctly) extract the foreign lambda  
>> > energy
>> > >> than it is to modify
>> > >> the actual exchange criterion. Erik did some work on foreign  
>> lambda
>> > >> calculations,
>> > >> but I don't know what the status of that is.
>> > >>
>> > >> I guess the head branch would be the better option, especially  
>> if > you
>> > >> want to run
>> > >> each replica over multiple cpu's.
>> > >
>> > > Maybe Erik can weigh in on whether this is "for sure", but my
>> > > understanding is that he's almost done with the "foreign lambda"
>> > > implementation (he indicated having a testable version over this
>> > > coming weekend).
>> >
>> > Yes, I'll start to send this to David & John for testing, but in a
>> > week or so we should have code for other people to play with too.
>> >
>> > Cheers,
>> >
>> > Erik
>>
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