[gmx-users] neighbor list

Sikandar Mashayak symashayak at gmail.com
Mon Jul 28 20:27:45 CEST 2014


I need to set up a simulation of LJ system, such that neighbor list is
built using grid algorithm with a cut-off of lj_cut_off + 0.1 every 20

So I am wondering what should be the accurate settings in the grompp.mdp

After reading the manual, I understand rvdw must be >= rlist. So how can I
specify rlist=lj_cut_off+0.1, should I use rlistlong?

Also, the cut-off scheme 'group' for simple LJ atoms with no charge, is it
equivalent to building neighbor list using atoms rather than group, since
each charge group will have only a single atom?


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