[gmx-users] Checking the existence of a hydrogen bond network
m.ebert at umontreal.ca
Thu Apr 16 21:16:25 CEST 2015
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,
> 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,
>> 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,
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