[gmx-users] coulombtype selection

[Kay Gottschalk]

I think for DNA you should use PME.

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
>
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Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
Herzl St. 1
Rehovot
Israel
+972-8-934 3639