[gmx-users] neighbor list

[Maria Nemirovskaya]

Hi,

I have a question about neighbor list construction. Is it correct that
the neighbor list is organized by charge groups? Ie an atom can be
within Rc but not in the list because its group is outside and the
other way around. Also, some solvents such as water are not in the
neighbor lists. Now, is there an option to build a neighbor list that
contains all atoms within Rc independent of their charge groups,
solvent type, etc? 

Thanks for your help,

Maria Nemirovskaya

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Maria Nemirovskaya
Postdoctoral Research Associate
Dept. of Chemistry, University of Oregon