[gmx-developers] file headers & nblists

Erik Lindahl lindahl at stanford.edu
Tue Jun 11 19:33:51 CEST 2002

Vishal Vaidyanathan wrote:
> 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.

I don't see any problem with adding it, the only question is which way 
is smartest; assume the official distribution is 'A', and there are two
groups using derived versions 'B' and 'C'. I don't see any obvious way
for group C to use files from group B without having their gromacs 
version too?

The easiest approach would of course be to add two fiels; one 
description string and an email adress. If the description strings don't
match we simply echo out the email adress and recommend you get in touch
with this person to find a version of grompp that supports your file...

It might not be a big problem though; we are planning to get rid of 
grompp and let mdrun read XML input/data/coordinate files automatically.

> 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
> 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.

Sounds interesting. By 'on the fly' I guess you mean 100% automated - 
could you expand the idea a bit?



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