[gmx-users] Average no of hbonds

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 6 16:19:37 CEST 2011

Steven Neumann wrote:
> On Tue, Sep 6, 2011 at 3:09 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
>     Steven Neumann wrote:
>         On Tue, Sep 6, 2011 at 2:50 PM, Mark Abraham
>         <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>
>         <mailto:Mark.Abraham at anu.edu.__au
>         <mailto:Mark.Abraham at anu.edu.au>>> wrote:
>            On 6/09/2011 11:37 PM, Steven Neumann wrote:
>                Dear Gromacs Users,
>                I am calculating hbonds between my 10 ligands and each
>                residue... How does Gromacs calculate average number of
>         hbonds
>                per timeframe?
>                Example:
>                for Glycine:
>                Av. num of hbonds/timeframe
>                0.96
>                To check whether that is correct I added all hbonds
>         formed with
>                Glycine during my simulation time over 2000 (each 50ps)
>                timeframes and I obtained value: 2900. If you divide it
>         by 2000
>                you will never get 0.96 obviously. How does Gromacs
>         calculate it?
>            Presumably by adding up the number in each time frame and
>         dividing
>            by the number. Unless you have a highly-exposed glycine, forming
>            more than one H-bond seems unlikely, and your 2900 number
>         suggests
>            it's happening lots of times. I expect you're comparing a sum of
>            oranges with a sum of apples, but without more information about
>            what you're doing in your attempt to check, we can't help much.
>            Please be sure to read g_hbond -h, and the legends of any
>         .xvg files
>            you're looking at.
>            Mark
>            Thank you Justin and Mark,
>          Yes, just found the mistake... I added pairs within 3.5 A
>         instead of hbonds so the Gromacs calculation is correct. So the
>         value is 0.96 for Glycine. So in this case it is a strong
>         interaction. Are there any criteria to assess strenght of
>         interactions or binding affinity for residues? Was it described
>         anywhere for each residue to specify these values with respect
>         to possible hbonds for each residue (e.g. Glycine - 3)?
>     Binding affinity can be determined from free energy calculations,
>     but for the case of multiple ligands this would be an incredibly
>     complex calculation (or series of calculations, really).  You might
>     be able to make some argument about occupancy of available hydrogen
>     bonding sites.
>     -Justin
> So will it be possible to exteract one ligand which from my 
> visualisation occupy one residue with highest number of av. hbonds 
> (others aggregate on bounded or bind weaker) and then calculate free energy?

Something like that might be possible, by calculating free energies over an MD 
rerun, but I've never tried it so I won't speculate.  Consult the literature for 
precedent and procedure and have a look at the free energy tutorial on the 
Gromacs site to see if you can piece it all together.  It won't be a trivial 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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