[gmx-users] coulombtype selection
kay.gottschalk at weizmann.ac.il
Tue Dec 21 08:26:13 CET 2004
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.
> Jian Zou
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Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
Herzl St. 1
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