[gmx-users] coulombtype selection

[David van der Spoel]

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.

> 
> On Dec 21, 2004, at 9:17 AM, Jian Zou wrote:
> 
> > Hi all,
> >
> > I'm doing simulation of dna in water.
> >
> > At first I choose for mdp option
> > nstlist = 5
> > rlist = 2.0
> > comlombtype = PME
> > rcoulomb = 2.0
> > rvdw = 2.0
> > fourierspacing = 0.1
> > optimize_fft = yes
> > But the simulation takes a long time (5 more days for 1ns run)
> >
> > Does PME is necessary for my charged system?
> > how about change to comlombtype = cutoff and reduce the cutoff?
> > How much will the change PME->cutoff reduce the accuracy?
> >
> > Thanks a lot in advance.
> >
> >
> > Regards,
> >
> > Jian Zou
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the www 
> > interface or send it to gmx-users-request at gromacs.org.
> >
> Dr. Kay-E. Gottschalk
> Department of Biological Chemistry
> Weizmann Institute of Science
> Herzl St. 1
> Rehovot
> Israel
> +972-8-934 3639
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++