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

[Justin A. Lemkul]

xuji wrote:
> 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
> "ROMACS 4.
>  
> 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?
>  

http://manual.gromacs.org/current/online/mdp_opt.html#nl

-Justin

> Appreciate any help in advance!
>  
>  
> 2010-06-17
> ------------------------------------------------------------------------
>  
> Best
>     wishes！
>  
> 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 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================