[gmx-users] fourier_nx and stuff

[Abil Aliev]

thanks, David, that was very helpful

 --- David <spoel at xray.bmc.uu.se> wrote: 
> On Mon, 2004-12-06 at 18:04 +0000, Abil Aliev wrote:
> > thanks, i missed zeros. what about the cut-off
> > distances? the manual.pdf suggests 0.9nm for all
> three
> > distances as an example for PME, but then insists
> on
> > 1.4nm at the end of the same chapter for gromos-96
> > force fields. 
> > 
> yes you want to have rlist = rcoulomb = 0.9 and rvdw
> = 1.4 and nstlist =
> 5
> 
> >  --- David <spoel at xray.bmc.uu.se> wrote: 
> > > On Mon, 2004-12-06 at 16:55 +0000, Abil Aliev
> wrote:
> > > > i have a box of protein and water sized 4.5 x
> 4.5
> > > x 18
> > > > nm. Would fourier_nx=fourier_ny=5 and
> > > fourier_nz=20 be
> > > > reasonable with pme_order=6 for this box size?
> > > > 
> > > No, you need roughly 0.1 nm spacing for
> pme_order=4.
> > > For a higher order
> > > you can use slightly large spacing, say 0.15 -
> 0.20.
> > > That would mean at
> > > least 30x30x120 for your box.
> > > 
> > > > with gromos-96 ff and pme, do we have to use
> > > > r(vdw)=1.4nm, r(coul)=r(list)=0.9nm OR all
> three
> > > r's
> > > > 0.9 nm and vdw-type=cut-off would suffice?
> > > > 
> > > > thank you in advance for your help. 
> > > >  
> > > > 
> > > > 
> > > > 		
> > > >
> > >
> >
>
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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
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> 755
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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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