[gmx-developers] Re: file headers & nblists

[Fan Hao]

> Hi All!
Hi, Vishal:

>   I'm in the process of implementing SASA based implicit solvent models
> gromacs and have a few questions:

Good idea, I am also working on implementing implicit solvent model
into gmx. It will based on generalized Born and SASA.

> 2) I have to implement a cut-off based calculation for the SASA (solvent
> accessible surface area). Could someone explain how I can use the
> neighbour list code to make two neighbour lists - one consisting of
> covalently bonded neighbours and one consisting of everything but
> covalently bonded neighbours, but within a certain cutoff. A very brief
> explanation of the nblist data structures (or even a quick ascii pointer
> diagram) would help me a long way here. I don't need to understand the
> details of the neighbour search, just the basic idea behind how the info
> is stored and how I should call init_nblist() or search_neighbours() in
> ns.c

Which SASA model will you use?
I have the same problem as you since the Richmond's model is precise
but quite slow. The cut-off method can be a good solution to that.
But there are other analytical models which are fast. You can get
approximated SASA without having cut-off.



Best regards

sincerely

Hao Fan :-)

-------------------------------------------------------------------------
Drs. Hao Fan                            email F.Hao at chem.rug.nl
Lab. of Biophysical Chemistry
University of Groningen
Nijenborgh 4                            9747 AG GRONINGEN
The Netherlands
-------------------------------------------------------------------------