I want to make h-bond analysis to show a formation and movement of an interface between two molecules (protein&RNA).
The common h-bond analysis gives me only a duration of it's life. But I need time frames, a plot of their durations on the time axis with points of formation and breaking of every bond.
How can I do this? Help me, please!
You can use g_hbond module. The following link provided a detailed tutorial for this module:
http://manual.gromacs.org/archive/4.6.4/online/g_hbond.html
You can also use VMD; the Hydrogen Bond modules of VMD (extensions -> analysis -> Hydrogen bonds or extensions -> analysis -> Timeline).
Thank you, but VMD gives me only timeline of quantity of bonds. How can I get more details?
If you use 'extensions -> analysis -> Hydrogen bonds', you can get more details in in output text file, such as, atoms involved in hydrogen bonds (donor and acceptor) and the start time (t0) and end time (tf) of each hydrogen bond (even in the case when the hydrogen bond between two atoms exists in different time intervals), so you are able to calculate the life time of each hydrogen bond.
1. Make a list of all possible hydrogen bonds.
2. Calculate distances and angles for all possible hydrogen bonds for each frame.
3. Determine the presence/absence of each hydrogen bond in every frame using cutoff values for the distances and angles.
4. Statistics, plots . . .
I`m sorry, but there are only donors, acceptors and occupancy in detailed information of h-bonds. Maybe I missed something in VMD hydrogen bond analysis?
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