xu zhijun wrote:
Thanks Justin.
You mean I put the na+ and Ca+ in the same "moleculetype"？
But I just worry about whether it is feasible to put the two ions in the
same moleculetypes even if they have no any connects between them (bond,
angle).
The chemical definition of a molecule and the Gromacs definition of a
moleculetype are completely unrelated. In theory, you could put all of the
molecules in your system in a single moleculetype. It's simply a topology
construct for organization.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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