[gmx-users] pdb2gmx -ff oplsaa -water tip4p / cut-offs for oplsa
spoel at xray.bmc.uu.se
Wed Dec 15 18:21:58 CET 2004
On Wed, 2004-12-15 at 16:32 +0100, Anton Feenstra wrote:
> David van der Spoel wrote:
> >>but the original JACS paper (1996,118,11228) talks about cutoffs of 15A
> >>for amides!? so if we are using PME, would rlist=rcoulomb=0.9 (no
> >>switching), rvdw=1.4 (cut-off) and nslist=5 be resonable with oplsa?
> > Yes, I use that routinely.
> And if I'd not want to use PME (e.g., for testing & benchmarking), is
> OPLS then normally used with simple cut-off or with a reaction field?
With a cut-off and VdW energy corrections (but not pressure
corrections). If you check Jorgensen's papers however, you will see that
he uses different cut-offs for different molecules. E.g. methanol and
ethanol with 1.1 nm and propanol with 1.5 nm. So much for
We have recently done an alcohol/water paper where we have used 1.1 nm +
PME. That worked "fine". (Wensink et al. JCP 119, 2003, p. 7308).
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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