[gmx-users] non-bonded interaction for molecule contain virtual site

zhonghe xu zhonghexu01 at 163.com
Thu Oct 10 15:06:47 CEST 2013

 Hi GMX users:

I am not sure when I prepared a itp file for molecule containing three virtual site by manual.
there is two  questions list below:
 1) whether it is validate when I set up bonded interaction(bond,angle or dihedral) between normal atom and virtual site ?
2) Is there any definition for generating non-bonded interaction between normal atom and virtual site,
as in "normal atom" which require neighboring atoms to be up to a certain number of bonds away.

Thanks in advance


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