[gmx-users] OPLS-AA and water

[David]

On Thu, 2004-10-07 at 21:13, Sichun Yang wrote:
> Hi Davie,
> 
> 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
> something else?
> If possible, could you address why position restraint all the heavy atoms
> is needed for OPLS since I am a newbie for OPLS?
No position restraints for production, just for equilibration of the
water.

> 
> 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?
> 
Just for bonds.


> Thanks and hope from you.
> 
> -Sichun
> 
> 
> 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
> > > > 
> > > > 
> > > > 
> > > > _______________________________________________
> > > > gmx-users mailing list
> > > > gmx-users at gromacs.org
> > > > http://www.gromacs.org/mailman/listinfo/gmx-users
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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.
> > ________________________________________________________________________
> > 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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> 
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-- 
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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