Hello
In a simple electrolyte I want to calculate the residence time of water molecules and anions within the solvation shell around cations. According to this
http://archive.ambermd.org/201809/0250.html I think I could use the hbond command, define WAT (or anion) as my mask and the cation as solventdonor/acceptor and set the distance to what I get from the RDF e.g. 3.25 Angstrom, but my input seems to be wrong (Amber16):
trajin ***.mdcrd
hbond Na-WAT out hbond-Na-WAT.dat :WAT dist 3.25 solventdonor :Na+ solventacceptor :Na+ avgout hbond-Na-WAT-avg.dat nointramol series uuseries hbond-Na-WAT-series.dat
go
lifetime hbond-Na-WAT-series[solutehb] out hbond-Na-WAT-lifetime.dat
go
Can anyone help me to get my input right?
Thanks in advance
David
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Received on Sun May 12 2019 - 04:00:02 PDT
