[gmx-users] g_hbond tool question

[Erik Marklund]

Dear Carlos,

You get a double contribution from MainChain and SideChain in this way, don't you?

Kind regards,
Erik

On 19 Nov 2014, at 03:00, Carlos Navarro Retamal <cnavarro at utalca.cl> wrote:

> Dear gromacs users,  
> I’m studying the hydrogen bond interaction between a protein and different solvents.To do that i’m using the g_hbond tools of gromacs (4.6.3 version).
> As groups,I started using ‘Protein’ and ‘Sol’ and i got an specific number.
> After that, to analyse the interaction in a more specific way between this 2 groups, i ran the g_hbond tools using different groups:
> 'MainChain+Cb' - 'SOL'
> 'MainChain+H'   - ‘SOL'
> 'SideChain'        -  'SOL'
> 'SideChain+H’   -  ‘SOL’
> But when i sum hbond got by these four selections i got different values (higher) than the values got from ‘Protein’ - ‘SOL’
> Why is this happening? Am i interpreting in a wrong way what the selection ‘Protein’ - ‘SOL’ is considering?
> Hope someone can help me.
> Thanks in advances,
> Carlos
> 
> 
> --  
> Carlos Navarro Retamal
> Bioinformatic engineer
> Ph.D(c) in Applied Science, Universidad de Talca, Chile
> Center of Bioinformatics and Molecular Simulations (CBSM)
> Universidad de Talca
> 2 Norte 685, Casilla 721, Talca - Chile   
> Teléfono: 56-71-201 798,  
> Fax: 56-71-201 561
> Email: carlos.navarro87 at gmail.com or cnavarro at utalca.cl
> 
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