[gmx-users] How to update the neighbor list heuristically?

xuji xuji at home.ipe.ac.cn
Thu Jun 17 04:38:09 CEST 2010

Hi all

In GMX4 paper 
"GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation" 

VIII. Other New Features. It says that
"Previously, GROMACS only supported neighbor list updates
at fixed intervals, but the use of potentials that are switched
exactly to zero at some finite distance is increasing, mainly
to avoid cutoff effects. To be sure that no interaction is
missed, the neighbor list can be updated heuristically in

And in IX. Benchmarks
It says that "The neighbor list was updated heuristically with a buffer of 0.26 nm."

But I don't known how to set the buffer size in the *.mdp file. Can someone give me an idea?

Appreciate any help in advance!



Ji Xu
The State Key Laboratory of Multiphase Complex System
Institute of Process Engineering
Chinese Academy of Sciences
Beijing 100190, China
Tel.: +86 10 8262 3713-804 
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