Hi,
I want to calculate water residence time near N+ as a fixed ionic group in my polymer system. Is there any direct way to calculate average residence time of water near N+? If not, could you please guide me how to do it? I found some clues but they were a bit confusing.
Thanks,in advance
You should define a distance for the "nearest water", for instance 5 amstrong, then you make an index where your atoms N+ would been defined. After that, you should use the tool "gmx select" and in the flag -selection you put 'SOL within 0.5 of N+'
This tool will count the number of water molecules nearby 5 amstrong of your N+ atoms as a function of time.
Dear M. Florencia Martini
Thank you very much for your help. Does this analysis perform residence time auto correlation function too? And, Can I get water residence time directly from the plot (number of water as a function of time) or not?
Thanks again
You should check out gmx hbond
https://manual.gromacs.org/2020.3/onlinehelp/gmx-hbond.html#gmx-hbond
dear Luis Fernando Cofas-Vargas
Thank you very much for your reply.
You could calculate the lifetime histogram with the flag -olt, in which shows the number of selected positions as a function of the time the position was continuously selected.
I hope this helps you.
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