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

[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
 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



  <https://mailtrack.io/> Sent with Mailtrack
<https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dilip@nitk.edu.in&idSignature=22>