[gmx-developers] BD + Poisson-Boltzmann forces?

[Vishal Vaidyanathan]

Hi,
   If you're unfamiliar with the gmx code, I'd say about a month. Actually
putting in the code and getting rid of compile time/run time errors will
take you about a couple of weeks, but getting the answers right will
probably take longer. Combine with Murphy's Law to get 2 months.

   On the other hand, the whole thing is conceptually quite simple - so it
might take only a couple of days, so don't let my estimate discourage you!
:-)

   If you want to discuss issues of implementation (what code to modify,
which data structures you'd need to access, etc), please feel free to
contact me personally or via this mailing list. I'm sure that would help
us both and perhaps some others trying something similar as well.

   At this time, I am not working on PB because I am stuck on a much
simpler model which is not producing expected results. Other
approaches including PB are scheduled  for the future though.

   Thanks,
								Vishal



On Tue, 3 Dec 2002, Oliver Beckstein wrote:

> Hello,
>
> I'd like to use Brownian dynamics with forces derived from the
> Poisson-Boltzmann (PB) equation (similar to UHBD, for example). As far as
> I know, Gromacs implements a BD integrator but the forces are straight
> electrostatics. However, there are packages like MEAD which could provide
> the PB potential grid to Gromacs.
>
> Is anyone already working on the implementation of PB in Gromacs (perhaps
> Vishal Vaidyanathan,
> http://www.gromacs.org/pipermail/gmx-developers/2002-June/000236.html) ?
> Or how difficult would it be to implement in the BD electrostatic forces
> derived from a potential grid (eg, supplied by MEAD)? Perhaps someone
> could provide a very rough estimate for the time required to code
> something like this? If it looks doable then I might attempt it.
>
> Cheers,
> Oliver
>
> --
> Oliver Beckstein * oliver at bioch.ox.ac.uk
>  http://indigo1.biop.ox.ac.uk/oliver/
>
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