Leila,
you didn't specify what you want exactly, but often what people want
is the number of waters in the first hydration shell. To get this, you
calculate an RDF of water oxygen around protein heavy atoms and
identify the first minimum. Then use a tool like g_dist to count the
number of waters within that distance. Do this for DNA and protein
separately, and then you might see that the number of waters in the
first hydration shell of these macromolecules decreases when they bind.
Chris.
-- original message --
Hi gromacs users
Since I study dynamic of interfacial water molecules between protein and
dna, I want to know, is there any keyword in gromacs to obtain number of
interfacial water molecules between protein and dna as a function of
simulation time? Is there any way which water molecules put in interface
between protein and dna?
any help will highly appreciated.
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