Re: PME or not PME? What happens if PME is turned off?

From: Chris Harrison (charris5_at_gmail.com)
Date: Wed Aug 03 2011 - 14:48:12 CDT

Can we see your config file?

On Tue, Aug 2, 2011 at 6:54 PM, esmael <haddadian_at_uchicago.edu> wrote:

> Hi,
>
> I tried using the "FullDirect yes" option using NAMD 2.8, but keep getting
> this error message
>
> "FATAL ERROR: Communicate::sendMessage not from Pe 0" Any suggestions?
>
> Thanks a lot,
> Esmael
>
>
> On Jul 19, 2011, at 2:45 PM, Chris Harrison wrote:
>
> > Actually, full electrostatics /is/ possible in NAMD. Use the
> > fullDirect keyword "FullDirect yes". But beware, this option is not
> > meant for production calculations as it is much slower than PME,
> > scaling as O(N^2).
> >
> > -Chris
> >
> >
> > On Mon, Jul 18, 2011 at 3:27 PM, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>
> wrote:
> >> Hi Bjoern,
> >>
> >> If you turn PME off, you are running cutoff electrostatics. Yes, it's
> >> faster. And fullElectFrequency becomes irrelevant : there is no full
> >> electrostatics.
> >>
> >> Cheers,
> >> Jerome
> >>
> >> On 18 July 2011 11:10, Bjoern Olausson <namdlist_at_googlemail.com> wrote:
> >>> Hi,
> >>>
> >>> I just happened to run a simulation with PME turned off.
> >>
> >>
> >
> >
> >
> > --
> > Chris Harrison, Ph.D.
> > Theoretical and Computational Biophysics Group
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
> >
> > char_at_ks.uiuc.edu Voice: 217-244-1733
> > http://www.ks.uiuc.edu/~char Fax: 217-244-6078
> >
>
>

-- 
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char               Fax: 217-244-6078

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