[gmx-users] Re: Re: [gmx-users] twin-range cut-offs and OPLS

[David van der Spoel]

On Thu, 2005-03-17 at 13:46 +0100, Marco Möller wrote:
> Dear David,
> 
> thank You very much for Your very fast response and answer!
> Might it be possible that You confused two of the parameters regarding 
> the PME section? You wrote:
> > rcoulomb            =  0.9
> > rvdw                =  1.4
> Isn' t it the other way round: 0.9 nm for rvdw, and 1.4 nm for rcoloumb?
> If it isn't a typing error, where should I read to understand why in the 
> PME algorithm the radius for coulomb forces can be so short, and why 
> still to expect vdw-force for such a long distance?
No it is correct. If you use PME, that takes care of the interactions
beyond 0.9 nm, in effect you don't have a cut-off anymore (for Coulomb).

So you take more Coulomb into account than you do Van der Waals. The mdp
options page on the website explains a bit, and so does the manual.

> 
> Best regards from Germany, and THANK YOU VERY MUCH for the GROMACS 
> package!
> 
> Marco.
> 
> Inst. f. Molekulare Biophysik
> Johannes Gutenberg - Universitaet
> 55118 Mainz, Germany
> moeller AT uni-mainz DOT de
> 
> 
> 
> 
> 
> ----- Original Message ----- 
> From: "David van der Spoel" <spoel at xray.bmc.uu.se>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Sent: Thursday, March 17, 2005 11:09 AM
> Subject: Re: [gmx-users] twin-range cut-offs and OPLS
> 
> 
> On Thu, 2005-03-17 at 10:34 퍝, Marco Möller wrote:
> > Dear All!
> >
> > I learned from the Gromacs User Guide and from some web tutorials 
> > about
> > MD how to use twin-range cut-offs for faster calculation of the
> > non-bonded interactions. The examples were given for the GMX force
> > field. As my aim is to do some first MD-runs on small peptides (13-23
> > aminoacids) to learn and catch up with the method of MD without 
> > wasting
> > to much computer time by using mindless parameters in the mdp files: I
> > appreciate any comments on the topic of choosing sensefull parameters 
> > to
> > bring a newbie on its MD way.
> >
> > My current parameters used with GMX-FF are
> > in a box whith a distance of 1.0 nm between box-edges and nearest
> > peptide atom:
> > rlist               =  0.8
> > coulombtype         =  cut-off
> > rcoulomb            =  1.4
> > rvdw                =  0.8
> > constraints         =  all-bonds
> > integrator          =  md
> > dt                  =  0.002
> >
> > If I want to use the Gromos96/SPC and particularly the OPLSAA/TIP5P
> > force-fields, can I just copy this parameters, or do I have to 
> > consider
> > some different boundary values? I read that it would be best to choose
> > the parameters in the range of values the force-fields were optimized
> > for, but up to now I did not found the information about which are the
> > perfect parameters with each of the Force-fields and nothing about
> > adopting them to the twin-range procedure.
> For production we use something like:
> rlist               =  0.9
> coulombtype         =  PME
> rcoulomb            =  0.9
> rvdw                =  1.4
> nstlist             =  5
> constraints         =  all-bonds
> integrator          =  md
> dt                  =  0.002
> 
> If you choose not to use PME you want to change rcoulomb to 1.4 as well.
> >
> > Thank You very much!
> > Marco Moeller
> >
> > ---------------
> > Marco Moeller
> > Inst. f. Molekulare Biophysik
> > Johannes Gutenberg - Universitaet
> > 55118 Mainz, Germany
> >
> > moeller AT uni-mainz DOT de
> >
> > _______________________________________________
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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
> ﯯ뻻ﯯ뻻ﯯ뻻ﯯ뻻ﯯ뻻ﯯ뻻ﯯ뻻ﯯ뻻ﯯ뻻
> 
> 
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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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