From: David Chalmers (david.chalmers_at_vcp.monash.edu.au)
Date: Tue Mar 30 2004 - 23:12:17 CST
Hi Brian & the list,
I only know the dogma that I have read that Ewald simulations should be
neutral (although I do remember reading _somewhere_ that this was less
important for the particle-mesh method). However, if somebody wanted to
do the experiment, they could compare radial distribution functions of
something like water with and without a neutral system. RDFs are quite
sensitive to the electrostatics of the system.
Otherwise, I just put in counter-ions.
David
On Tue, 30 Mar 2004, Brian Bennion wrote:
>
> Your are correct in thatPME by some definition requires a neutral system.
> However, as I posted earlier, my runs with PME on with and without a
> neutral system were identical as far as bulk properties of temp or
> pressure under NVE.
> I don't know enough about PME implementations to know what else to look
> for.
>
> Regards
> Brian
>
> On Tue, 30 Mar 2004, himanshu chandola wrote:
>
> > hi all -
> > subsequently to the discussion on counterions : what if i start a pme
> > simulation using particle ewald summation method without adding
> > counterions.Does namd include a background charge if the system is not
> > neutral and running ewald summation? Has anyone tried running an namd
> > simulation using particle ewald without neutralizing the system?
> >
> > I guess particle ewald requires a neutral system but has anyone tried
> > running simulations without neutralizing the system in whole?
> >
> > himanshu
> >
> > ---------------------------------------------------------------------
> > "Blessed are the geek
> > for they will inherit the shell
> >
> >
> > -- Fritz, 5:5"
> >
>
> *****************************************************************
> **Brian Bennion, Ph.D. **
> **Computational and Systems Biology Division **
> **Biology and Biotechnology Research Program **
> **Lawrence Livermore National Laboratory **
> **P.O. Box 808, L-448 bennion1_at_llnl.gov **
> **7000 East Avenue phone: (925) 422-5722 **
> **Livermore, CA 94550 fax: (925) 424-6605 **
> *****************************************************************
>
>
_____________________________________________________________________________
David Chalmers Lab: 9903 9110
Victorian College of Pharmacy Fax: 9903 9582
381 Royal Pde, Parkville, Vic 3053
Australia David.Chalmers_at_vcp.monash.edu.au
_____________________________________________________________________________
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:38:32 CST