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

2017-05-30 Thread Nikhil Maroli 
Hi,
I suggest you use MDAnalysis package, in which built in Python code is
available.

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Nikhil Maroli
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Re: [gmx-users] Regarding python program/code for Hydrogen bond lifetime

2017-05-30 Thread 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 
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
>  28SOLHW1  116   1.520   0.524   1.293
>  28SOLHW2  117   1.645   0.519   1.187
>  29SOL OW  118   0.135   0.791   1.373
>  29SOLHW1  119   0.168   0.716   1.316
>  29SOLHW2  120   0.190   0.873   1.355
>  30SOL OW  121   0.279   0.419   0.486
>  30SOLHW1  122   0.366   0.400   0.440
>  30SOLHW2  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
>  28SOLHW1  116   1.520   0.524   1.293
>  28SOLHW2  117   1.645   0.519   1.187
>  29SOL OW  118   0.135   0.791   1.373
>  29SOLHW1  119   0.168   0.716   1.316
>  29SOLHW2  120   0.190   0.873   1.355
>  30SOL OW  121   0.279   0.419   0.486
>  30SOLHW1  122   0.366   0.400   0.440
>  30SOLHW2  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
>  28SOLHW1  116   1.520   0.524   1.293
>  28SOLHW2  117   1.645   0.519   1.187
>  29SOL OW  118   0.135   0.791   1.373
>  29SOLHW1  119   0.168   0.716   1.316
>  29SOLHW2  120   0.190   0.873   1.355
>  30SOL OW  121   0.279   0.419   0.486
>  30SOLHW1  122   0.366   0.400   0.440
>  30SOLHW2  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
>
>
>
>    Sent with Mailtrack
> 
>



-- 
With Best Regards,

DILIP.H.N
Ph.D Student
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[gmx-users] Regarding python program/code for Hydrogen bond lifetime

2017-05-30 Thread Dilip H N 
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
 28SOLHW1  116   1.520   0.524   1.293
 28SOLHW2  117   1.645   0.519   1.187
 29SOL OW  118   0.135   0.791   1.373
 29SOLHW1  119   0.168   0.716   1.316
 29SOLHW2  120   0.190   0.873   1.355
 30SOL OW  121   0.279   0.419   0.486
 30SOLHW1  122   0.366   0.400   0.440
 30SOLHW2  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
 28SOLHW1  116   1.520   0.524   1.293
 28SOLHW2  117   1.645   0.519   1.187
 29SOL OW  118   0.135   0.791   1.373
 29SOLHW1  119   0.168   0.716   1.316
 29SOLHW2  120   0.190   0.873   1.355
 30SOL OW  121   0.279   0.419   0.486
 30SOLHW1  122   0.366   0.400   0.440
 30SOLHW2  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
 28SOLHW1  116   1.520   0.524   1.293
 28SOLHW2  117   1.645   0.519   1.187
 29SOL OW  118   0.135   0.791   1.373
 29SOLHW1  119   0.168   0.716   1.316
 29SOLHW2  120   0.190   0.873   1.355
 30SOL OW  121   0.279   0.419   0.486
 30SOLHW1  122   0.366   0.400   0.440
 30SOLHW2  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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