[gmx-users] OPLS-AA and water
syang at physics.ucsd.edu
Thu Oct 7 21:13:46 CEST 2004
I also read your paper. I have a couple of questions you haven't addressed
in the method section.
First, for the pre-production simulation, you mention you used position
restraint with force constant of 1000 [unit] to relax the system.
But what kind of position restraints did you use for the production runs?
Did you use the default, i.e., position restraint all the heavy atoms with
force constant of 1 [unit] as desribed by the file 'posre.itp', or
If possible, could you address why position restraint all the heavy atoms
is needed for OPLS since I am a newbie for OPLS?
Second, in term of constraint, did you use the constraint for both bond
and angle in the harmonic potential or the constraint for all-bonds?
Thanks and hope from you.
On Thu, 7 Oct 2004, David van der Spoel wrote:
> On Thu, 2004-10-07 at 07:16, Y U Sasidhar wrote:
> > David L. Bostick wrote:
> > > Does anyone know if the OPLS-AA force field for proteins can be used with
> > > SPC water? .. Or is it optimized only for use with TIP3P? Since the force
> > > field comes from Jorgensen, I thought it might be only for TIP3P.
> > >
> > > Thanks,
> > > David
> > >
> > >
> > >
> > > _______________________________________________
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> > I remeber seeing a very recent science paper which uses opls
> > with spc.
> Erik Lindahl and me did some tests, and we found that it works better
> with TIP4P, see J. Phys. Chem. B. 117 pp. 11178-11187 (2003)
> 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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