Hi,
Any documentation on how this is actually done?
Sounds interesting!
XAvier.
On Jan 28, 2009, at 11:12 PM, LuLanyuan wrote:
Hi Berk,
Thanks very much. I've found the problem. As you said I forgot to
increase rvdw. So the buffer is zero and the system needs to update
the nblist every step, which is obviously wrong. After I corrected
the mistake, the speed for "nstlist=-1" is roughly three times
faster as I expected.
Lanyuan
From: [email protected]
To: [email protected]
Subject: RE: [gmx-users] "nstlist=-1" and performance problem
Date: Wed, 28 Jan 2009 10:42:59 +0100
Hi,
I assume you did not only change nstlist, but also other mdp
settings, or not?
Changing only nstlist from 1 to -1 should result in nearly equal or
much faster speeds.
For efficient simulations with nslist=-1 you need to set an
appropriate
buffer region (rlist > rcoulomb=rvdw). In 4.0 you have to optimize
this by hand.
It would be nice to have this automated.
At the end of the log file (a run of a few minutes is enough) you
can see what
the neighborlist lifetime is. Optimal is usually something between
10 and 20.
Play with rlist to optimize the performance (also printed at the end
of the log file).
Berk
From: [email protected]
To: [email protected]
Date: Mon, 26 Jan 2009 17:31:43 -0500
Subject: [gmx-users] "nstlist=-1" and performance problem
Hello,
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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