From: himanshu chandola (beu99419_at_ccsun50.iitd.ac.in)
Date: Wed Mar 31 2004 - 03:13:51 CST
thanks for the info brian. i made much of my setup without the
counterions - so i guess i'll just go ahead without putting them hoping
that the simulation wouldn't break in between.
regards
himanshu
---------------------------------------------------------------------
"Blessed are the geek
for they will inherit the shell
-- Fritz, 5:5"
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 **
> *****************************************************************
>
>
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