[gmx-users] on the "tc-grps = Protein Non-Protein ; two coupling groups" in the on-line tutorial

Acoot Brett acootbrett at yahoo.com
Wed Apr 11 20:52:38 CEST 2012

Dear All,
In the on-line tutorial of Justin Lemkul (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html) for both lysozyme and the umbrella sampling, in the npt.mdp, there is "tc-grps         = Protein Non-Protein   ; two coupling groups".
In the system of lysozyme, the system contains protein, SOL and CL-. In the system of umbrella sampling, the system contains protein, SOL, Na+ and CL-.
Correspondingly will you please explain to me how "Non-Protein" group should be defined?
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