Gromacs

Neighborlist-Update

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    Dynamically updated neighborlists. Instead of updating every nstlist, regardless of whether there was movement out or in of the cutoff distance, the distance each particle moves can be calculated, and then updating occurs if any particle has moved too far.

    Right now, if there are violations of the cutoffs between neighbor list updates, we don't really know about it. It would be better for energy conservation to have an option for these updated to be performed on a need basis. If rlist is R_list, and the cutoff is R_cut, then after each step, the distances that each particle has moved can be calculated. if any of these distances is more than (R_list - R-cut)/2, then the neighbor lists should be updated at some point before the next energy calculation.

    A basic implementation of this algorithm should be very simple, but a parallel version might be a bit harder -- I don't know enough about how GROMACS works in parallel to know how feasible it would be, or the safeguards that would need to be put in place to avoid slowing things down.

    Berk has implemented this in the CVS code (head branch).
    Page last modified 18:03, 21 Mar 2009 by rossen