[gmx-developers] file headers & nblists

Vishal Vaidyanathan vvishal at stanford.edu
Tue Jun 11 12:38:06 CEST 2002

Hi All!

  To the gmx developers: gmx is AMAZING! Thank you SO MUCH for this
fantastic program!!

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

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.

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

3) Is a gmx "builder" in the works by any chance? For design work, I am
going to implement (after the implicit solvent models are done and tested)
a program to generate/mutate structures on the fly. Any suggestions or
comments are welcome.


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