[gmx-users] fourier_nx and stuff

[David]

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
> > phone:  46 18 471 4205          fax: 46 18 511 755
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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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