[gmx-users] use of g_hbond

[K.A. Feenstra]

Valentin Gogonea wrote:
> I am trying to use the g_hbond analysis tool on a box containing the 
> cpeptide (from the gmxdemo folder) to calculate the hydrogen bonds. I 
> used g_hbond on a 2 ps trajectory of cpeptide in water (tip4p) selecting 
> the System as first and second group:
> 
> g_hbond -debug -s cpeptide_md -f cpeptide_md
> 
> I got the following error message:
> 
> Select a group: 1
> Select a group: 1
> Calculating hydrogen bonds in one group of 216 atoms
> Found 30 donors and 41 acceptors in group 'Protein'
> trn version: GMX_trn_file
> Reading frame       0 time    0.000   Bus error
> 
> 
> I am using the pre-release version 3.1.5 (provided by Erik).
> 
> Can anybody tell me what may be the problem?

Just a quick guess: g_hbond might rely on some assumptions that only
hold for SPC, and not for tip4p... ?


-- 
Groetjes,

Anton
  ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
| |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
|   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
| (    ) |-----------------------------------------------------------|
|  \__/  | "If You See Me Getting High, Knock Me Down"               |
|        | (Red Hot Chili Peppers)                                   |
|________|___________________________________________________________|