[gmx-users] Checking the existence of a hydrogen bond network

[Ebert Maximilian]

Hey Erik,

Just wanted to thank you. This is exactly what I was looking for. Never looked at the end of the ndx file. Just a question regarding the index. If I am not mistaken the first entry of bond registry entry:

[ hbonds_Water-r_216_r_244 ]
   4216   4217   3342
   7225   7226   2962

should correspond to the last entry in the xpm file matrix:

/* y-axis:  0 1 2 3 4 5 6 7 8 9 10 11 12 */
" oo ooooooooo  ooo oo  oo  ooo ooo oooooo    o o oo  o   o ooo ooo oo   o    o     o                 “,
"ooooo                                    o                                                           “


and hence the last bond entry (7225   7226   2962) corresponds to the line beneath the y-axis entry? Just to be sure.

Have a great day,

Max

> On Apr 16, 2015, at 11:28 AM, Erik Marklund <erik.marklund at chem.ox.ac.uk> wrote:
> 
> Dear Max,
> 
> You will need to use the -hbm and -hbn options to generate the existance function for all hydrogen bonds over time. Parsing those files requires a bit of work, but is certainly doable.
> 
> Kind regards,
> Erik
> 
>> On 16 Apr 2015, at 12:59, Ebert Maximilian <m.ebert at umontreal.ca> wrote:
>> 
>> Dear list,
>> 
>> I am trying to find a possibility with standard gromacs tools to verify in every frame if two residues are interconnected through a hbonds with a water molecule. My initial idea was to evaluate the hbonds of both residues per frame and write a small bash script looking for frames in which both residues hbonded with the same water molecule. However, I could’t find an option in gmx hbond to write out the hbonds per frame except for the number of hbonds per frame and a file with all partners. Before starting to have to loop over every frame individually and start gmx hbond as often as the number of frames I wanted to know if there is an easier approach to what I want to do.
>> 
>> Basically I want to know how long this bridge existed over the course of the simulation.
>> 
>> Thank you very much,
>> 
>> Max
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