[gmx-users] Segmentation fault from g_hbond

Nuno R. L. Ferreira nunolf at ci.uc.pt
Fri Apr 9 16:37:01 CEST 2004

xiaobing tian <xiaobingtian at yahoo.com> escreveu:

> Dear GMX users,
> After 1ns MD for my system (protein+drug(RPR)+ Ca2+ +
> Cl-), g_hbond -f file.xtc -s file.tpr -num hydrogen.xvg  
> gave a Segmentation faut (see attached file below) and
> then stopped. How to fix the problem?( I use gmx3.2.1,
> Linux Red Hat8.0) 

> Checking for overlap...
> Calculating hydrogen bonds between two groups of 42
> and 2869 atoms
> Found 4 donors and 7 acceptors in group 'RPR'
> Found 419 donors and 817 acceptors in group 'Protein'
> Going to allocate 8169 kb of memory,  and that's only
> the beginning

Do you have enough memory?

Nuno Ricardo Santos Loureiro da Silva Ferreira
Ph.D student
Grupo de Química Biológica
Departamento de Química
Faculdade de Ciências e Tecnologia
Universidade de Coimbra
3004-535 Coimbra
\" Do not worry about your dificulties in mathematics.
  I can assure you that mine are still greater.\"

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