[gmx-users] "nstlist=-1" and performance problem

LuLanyuan lulanyuan at msn.com
Mon Jan 26 23:31:43 CET 2009

Could Berk or someone else answer my question regarding the new "nstlist=-1" option in gmx4? In my understanding, the algorithm for this option is the one used in DLPOLY/LAMMPS. However, When I was trying two gromacs runs with "nstlist=-1" and "nstlist=1", I found the speeds were basically the same. Isn't this automatic nblist checking supposed to be faster than updating the nblist every step? I also did similar tests on LAMMPS for the same system and found the speed for automatical updating was several times faster. As a result, although Gromacs is about 60% faster if we choose nstlist=1,  it's much slower than LAMMPS if we choose the automatic nblist updating. 
Thanks in advance for any ideas about it.
Lanyuan Lu

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