[gmx-users] coulombtype selection
spoel at xray.bmc.uu.se
Tue Dec 28 08:51:17 CET 2004
On Tue, 2004-12-28 at 14:55 +0800, Jian Zou wrote:
> Prof. Spoel,
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] coulombtype selection
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1103616643.9622.0.camel at vangogh>
> Content-Type: text/plain
> On Tue, 2004-12-21 at 09:26 +0200, Kay Gottschalk wrote:
> >> I think for DNA you should use PME.
> > Yes, but you can definitely change the cut/offs to 0.9/1.4 for vdw and 0.9
> > for Coulomb.
> > That will speed up a factor of 8.
> OK, PME should be used for my case.
> I tried this cutoff but the simulation failed due to "pressure scaling more
> than 1%".
> I also tried 1.0/1.5 for vdw and 1.0 for coulomb, failed again due to the
> same reason.
> When I change the cutoff to 1.0/2.0 for vdw and 1.0 for coulomb, the
> simulation runs.
> Should I do further EM or PR before MD if I still want to reduce the cutoff
> to save time? Or I should remove P coupling?
First check your starting structure and topology, second increase tau_p
to e.g. 5 ps and check the compressibility (should be roughly 5e-5).
> Thanks a lot in advance.
> Jian Zou
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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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