[gmx-users] pdb2gmx -ff oplsaa -water tip4p / cut-offs for oplsa

[David]

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
transferability.

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.
________________________________________________________________________
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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