AMBER Archive (2008)

Subject: RE: AMBER: Bennett acceptance ratio with Amber10

From: steinbrt_at_scripps.edu
Date: Wed Aug 27 2008 - 11:28:13 CDT

Hi Samuel,

from my (limited) understanding of what is necessary for BAR-evaluation,
you need to compute dVdl at a given timestep for multiple lambdas and form
a histogram from these values. This will require a little work to put into
the amber-code, but if you can write something that does that as a
postprocessing step of your trajectories, I guess it should work. Of
course, unless you saved your trajectories at every step, you will
drastically reduce the number of datapoints you get from doing a free
energy calculation this way...

Regards,

Thomas

> Hello, Thomas
>
> Even if it is not implemented at the moment I guess I can implement some
> code by myself. However, I still would like to know if I can use the
> trajectories from my TI simulations, to get the values I need to compute
> the Bennett acceptance ratio. I'm not sure what information the mdcrd file
> contains for the V0 and V1 states, and if I can use some code of mine to
> calculate the potential energy along the trajectories, in order to compute
> the Bennett acceptance ratio. I would like you to tell me if it is
> possible from a theoretical point of view, sort to say.
>
> Hope I made myself clear,
> Kind regards,
> Samuel
>
>
> -----Original Message-----
> From: owner-amber_at_scripps.edu on behalf of steinbrt_at_scripps.edu
> Sent: Tue 8/26/2008 3:45 PM
> To: amber_at_scripps.edu
> Subject: Re: AMBER: Bennett acceptance ratio with Amber10
>
> Hi Samuel,
>
> unfortunately, the Bennett acceptance ratio method is not implemented in
> the Amber TI code at the moment. It is on the list of things to maybe be
> put into it in the near future, though.
>
> Kind Regards,
>
> Thomas
>
>>
>> Hello, Amber users
>>
>> I would like to know if it is possible to use the Bennett acceptance
>> ratio
>> method with Amber 10 to calculate free energy differences? I'm aware
>> about
>> the theory behind the method but I would like to know how to set up the
>> systems in Amber 10.
>>
>> I've started a project were I've calculated dG of some ligand-protein
>> systems using TI and by using the scheme in the TI tutorial for Amber
>> 10.
>> Is it possible to use some data or the trajectories from these
>> simulations
>> when calculating the Bennett acceptance ratio? Is it gonna work with the
>> soft-core potentials?
>>
>> Best regards,
>> Samuel Genheden
>> Lund university, Sweden
>>
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu