[gmx-users] comparison of reaction field and PME
David van der Spoel
spoel at xray.bmc.uu.se
Mon Mar 4 19:54:56 CET 2002
On Mon, 4 Mar 2002, Yuguang Mu wrote:
>I have a little experience of AMBER package, there using PME
>a little slower that CUT-OFF.
But in both cases, gromacs is considerably faster. The difference in speed
is due to the more complex innerloop. Also, you can reduce the cut-off for
Coulomb when using PME (e.g. to 0.9) while you keep the LJ at 1.2. This
will give you the same Coulomb forces as when using 1.2, but much faster.
The LJ forces between 0.9 and 1.2 are only updated when you do
neighboursearching (recommend nstlist = 5).
Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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