[gmx-users] Regarding python program/code for Hydrogen bond lifetime

[Dilip H N]

Because in the command gmx h_bond it is not calculating Continuous hydrogen
bond correlation function



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On Tue, May 30, 2017 at 10:58 PM, Dilip H N <cy16f01.dilip at nitk.edu.in>
wrote:

> I have ran a simulation and extracted the trajectory for t=0.5 ps each in
> gromacs. The trajectory file is as follows..
>
> Generated by trjconv : Glycine-Ammonia-Water t= 0.500
>  28SOL     OW  115   1.586   0.579   1.240
>  28SOL    HW1  116   1.520   0.524   1.293
>  28SOL    HW2  117   1.645   0.519   1.187
>  29SOL     OW  118   0.135   0.791   1.373
>  29SOL    HW1  119   0.168   0.716   1.316
>  29SOL    HW2  120   0.190   0.873   1.355
>  30SOL     OW  121   0.279   0.419   0.486
>  30SOL    HW1  122   0.366   0.400   0.440
>  30SOL    HW2  123   0.204   0.415   0.41
> .
> .
> .
>
> Generated by trjconv : Glycine-Ammonia-Water t=  1.000
>  28SOL     OW  115   1.586   0.579   1.240
>  28SOL    HW1  116   1.520   0.524   1.293
>  28SOL    HW2  117   1.645   0.519   1.187
>  29SOL     OW  118   0.135   0.791   1.373
>  29SOL    HW1  119   0.168   0.716   1.316
>  29SOL    HW2  120   0.190   0.873   1.355
>  30SOL     OW  121   0.279   0.419   0.486
>  30SOL    HW1  122   0.366   0.400   0.440
>  30SOL    HW2  123   0.204   0.415   0.41
> .
> .
> .
>
> Generated by trjconv : Glycine-Ammonia-Water t=  10.000
>  28SOL     OW  115   1.586   0.579   1.240
>  28SOL    HW1  116   1.520   0.524   1.293
>  28SOL    HW2  117   1.645   0.519   1.187
>  29SOL     OW  118   0.135   0.791   1.373
>  29SOL    HW1  119   0.168   0.716   1.316
>  29SOL    HW2  120   0.190   0.873   1.355
>  30SOL     OW  121   0.279   0.419   0.486
>  30SOL    HW1  122   0.366   0.400   0.440
>  30SOL    HW2  123   0.204   0.415   0.41
> .
>
> Can anybody suggest ideas to write a python program/code to calculate the
> hydrogen bond (continuous/intermittent) time correlations..ie., hydrogen
> bond if it exists between oxygen of one water molecule with hydrogen of
> other water molecule at a distance less than 2.45 angstrom or between
> oxygen of one water molecule with oxygen of other water molecule at a
> distance less than 3.5 angstrom.
>
> Any suggestions regarding this...
>
> Thank you
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
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>



-- 
With Best Regards,

DILIP.H.N
Ph.D Student