[gmx-developers] implicit solvent free energy

[Mark Abraham]

Also note that I fixed some of the grosser errors made in the 4.6
transition in http://redmine.gromacs.org/issues/1237, but any progress
is stalled until someone is interested enough that we have some
equations for how GB stuff varies with lambda, etc.

Mark

On Fri, Aug 30, 2013 at 9:52 AM, Erik Lindahl
<erik.lindahl at scilifelab.se> wrote:
> Hi David,
>
> Let me phrase it this way: We would certainly be happy to make the GB code
> very efficient, and make sure that it works well in domain decomposition
> too, if other people/developers are interested in doing the work to make
> sure it results in accurate free energies, test and tune how different GB
> implementations work with screening, and in general help provide a clear set
> of cases where it is obviously useful.
>
> The biggest problem with GB is that it is difficult to get it efficient for
> standard simulations where you want long trajectories. Part of this comes
> from the current efficiency of explicit-solvent, but the main issue is that
> GB by definition will never be able to scale as efficiently as explicit
> solvent simulations (both due to spatial inhomogeneity, longer-range
> interactions, and several communication and separate kernel executions
> during force evaluation where things cannot be perfectly load-balanced).
> Unfortunately, this will only get worse the more you parallelize, and that
> seems to be the road ahead.
>
> The one place I see where GB might be competitive would be rapid screening
> applications, in particular when you can stay on a single node for each
> compound.
>
> So, to sum it up: If somebody would be willing to help discuss the equations
> we want to implement, and assist with all the testing, I'm sure we could
> find an interesting joint project where we get it implemented!
>
> Cheers,
>
> Erik
>
>
>
>
>
> On Aug 30, 2013, at 8:52 AM, Gerrit Groenhof <ggroenh at gwdg.de> wrote:
>
> Hi David,
>
>
> In any case:
> - Are other people similarly interested in this?
>
>
>
> Not in implementing, but having the GB code working in combination with free
> energy could be of interest when one wants to address the effects of
> periodicity and background charge on the free energy. Just not sure if tis
> would be worth the effort of maintaining the GB code, but I might use it.
>
> Best,
> Gerrit
>
> - Are there any efforts underway to get the GB code to work properly with
> free energy?
> - What are the problems/obstacles?
>
> Thanks!
> David
>
>
> --
> David Mobley
> dmobley at gmail.com
> 949-385-2436
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