[gmx-developers] file headers & nblists

[Anton Feenstra]

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

Great! Although I am not a believer in implicit solvents, it would
be nice to have them as comparison, or for certain cases where they
do work.

> 1) Would it be possible (useful?) for the official gromacs file headers to
> include an extra string field besides the version number that can be used
> by different groups working on gromacs to identify their own specific file
> types? That would make it possible for groups to develop and distribute
> gromacs mods that may not be included in the official gromacs distrib, but
> still be compatible with official gromacs files or atleast warn the user
> that they are using the wrong file/program combo?
>    I am not sure using large version numbers for this purpose will be as
> straightforward as using a small string id.

That sounds like official support for officially unsupported versions
;-)

Somehow, I don't like the idea. Additional features shouldn't interfere
with the 'basics' in such a way that things get incompatible. (Also for
your own sake I would advise against it, it gets very confusing!) So
as long as additions and/or modifications are compatible with what's
already there, it shouldn't matter which version (official, or local
hack or whatever) you use; same input -> same output. (Unless you turn
on something new by default ofcourse, but there you should also be
very conservative, imho.)

> 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

g_hbond uses the nblist code for finding h-bonds, so you could
look into the g_hbond code and see how it's done. At least that
would be easier to read than the mdrun code... ;-)

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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