[gmx-users] Segmentation fault from g_hbond

[Nuno R. L. Ferreira]

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) 
> 

[...snip...]
> 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?





-- 
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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
Portugal
www.biolchem.qui.uc.pt
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\" Do not worry about your dificulties in mathematics.
  I can assure you that mine are still greater.\"
                                       e=mc2
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