GROMACS version: 2018
GROMACS modification: No
I wanted to analyze the lifetime of water molecules in the active site
(i.e. within a distance of 0.5 A of a electrophile C atom) and was
wondering if there’s a way implemented in GROMACS to do this. It seems that ‘gmx hbond’ has something like this implemented. However, in
my case I want the lifetime defined between water molecules and a certain
C atom, and not N or O atoms.
I’ve seen in the Amber emails that Aqua-duct (http://www.aquaduct.pl/)
might be able to do that, but would be still interested to hear if Gromacs
has its own solution to that.
Thanks a lot in advance!