[AMBER] Residence time around ions

From: Reber, David <David.Reber.empa.ch>
Date: Sun, 12 May 2019 10:58:43 +0000

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
lifetime hbond-Na-WAT-series[solutehb] out hbond-Na-WAT-lifetime.dat

Can anyone help me to get my input right?
Thanks in advance

AMBER mailing list
Received on Sun May 12 2019 - 04:00:02 PDT
Custom Search