Hi,
> How can we calculate water survival probability?
Since atoms aren't created or destroyed in an MD simulation, the
probability of survival is 100%.
All joking aside, are you talking about lifetime or occupancy (i.e.
how long a water remains bound to a certain spot)? In that case you
may want the 'hbond' command with 'series' and
'solventdonor'/'solventacceptor' keywords to generate hydrogen bond
time series data, followed by 'lifetime' analysis to measure the
lifetime of 'bound' states. A very very basic example of this is given
in the following tutorial:
https://amberhub.chpc.utah.edu/hydrogen-bond-analysis-within-a-protein/
-Dan
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Received on Sun Mar 12 2023 - 08:00:03 PDT
