Re: FEP: delta_G, memory of Hamiltonians corresponding to last G value?

From: Sebastian Stolzenberg (s.stolzenberg_at_gmail.com)
Date: Thu Oct 09 2008 - 18:01:13 CDT

Dear Jerome,

thank you for your quick reply.
> As a side note: some greatly improved FEP code has been making its way
> into CVS lately. If you are not afraid of compiling NAMD, you might
> want to have a look.
>
>
what does "greatly improved" mean?
My aim is to implement a flexible delta_lambda-step-FEP, meaning the
script will wrap around the NAMD-FEP and try to adjust delta_lambda
"on-the-fly" based on the degree of equilibration and the free-energy
change.
I have to wait for a day to get access to CVS - Am I trying to reinvent
the wheel here?

Thanks a lot,
Seb

> Best,
> Jerome
>
> On Thu, Oct 9, 2008 at 3:10 PM, Sebastian Stolzenberg
> <s.stolzenberg_at_gmail.com> wrote:
>
>> Dear All,
>>
>> in NAMD-FEP, say, I execute the command
>>
>> runFEPlist {.001 .01 .1} $numSteps
>>
>> After having calculated delta_G(.001)=G(.01)-G(.001) with exponential
>> averages of Hamiltonians, will NAMD "memorize" the Hamiltonians
>> corresponding to G(.01) when next calculating
>> delta_G(.01)=G(.1)-G(.01)? Or
>> will it re-measure the Hamiltonians corresponding to G(.01) and then
>> proceed
>> to calculate G(.1) and delta_G(.01)?
>>
>> Thank you,
>> Best,
>> Sebastian
>>
>>
>>

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