[gmx-users] fourier_nx and stuff
spoel at xray.bmc.uu.se
Mon Dec 6 18:49:04 CET 2004
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 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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