Re: Is it necessary to neutralize the system with NAMD program?

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Tue Mar 16 2004 - 16:58:52 CST

No doubt, dna/rna need the counterions or you will have some serious
problems.

in an ideal MD world our systems would be 5mM Glucose, XXmM NaCl, XXmM
KCl, 100mM Protein, etc......

On Wed, 17 Mar 2004, Aaron Oakley wrote:

> My experience mirrors Brian's.
> I've done several simulations > 1ns,
> using PME with and without counterions
> with no overall differences.
>
> However, I think it would be important
> to include counterions where DNA/RNA
> are involved, because of the concentration of
> charge near the nucleotide backbone.
> Can anyone comment on this?
>
> Cheers,
>
> Aaron
>
> On 17/03/2004, at 6:07 AM, Brian Bennion wrote:
>
> >
> > I read the same email message on ccl.
> >
> > I have thought about this problem as well and have tested systems both
> > ways.
> >
> > I was taught that ions, unless specifically needed in the protein
> > structure, were superflous. The water screens the charge on any ion
> > within 4-6 angstroms. However, these simulations were not using PME.
> >
> > My results with and without counterions are equivalent. (ie temp,
> > pres,
> > gpress values are within 1-2% at 0.25ns and 11.0ns for a system with
> > 65K
> > atoms and a net +3 charge.
> >
> >
> > If any one else has a contrary info I would love to here it.
> >
> > If you choose to add counter ions, the vmd plugin autoionize might be
> > what
> > you need.
> >
> > Regards
> > Brian
> >
> > PS
> > Contrary to what the ccl list member said. We are not even close to
> > real-life conditions even without PBC. Thats what ab-initio MD is for!!
> >
> >
> >
> >
> > On Sun, 14 Mar 2004 yxiong_at_mail.ccnu.edu.cn wrote:
> >
> >> Dear sir,
> >> I have doing MD at a charged system with PME method and Periodic
> >> Boundary
> >> Conditions.
> >> I see the information as following in CCL mailing list:
> >> --------------------------------------------------------------
> >> When you use periodic boundary conditions, you are effectively
> >> simulating an infinite system. With a non-zero total charge, you then
> >> get an infinite total charge and an infinite potential energy. Such a
> >> system would not be stable under real-life conditions (i.e. without
> >> the
> >> artifact of periodic boundary conditions). In fact, if you simulate
> >> such a system at constant pressure, i.e. with a variable box size, you
> >> will see the volume go up systematically.
> >> -----------------------------------------------------------------
> >> I want to get the geometry of system. Is it necessary to neutralize
> >> the
> >> system with NAMD program? If yes, how can I neutralize the system
> >> easily?
> >>
> >> Thank you for your advice!
> >>
> >>
> >>
> >
> > *****************************************************************
> > **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 **
> > *****************************************************************
> >
> >
> ---------------------------------------------------------
> Structural Biology Group
> Research School of Chemistry
> Australian National University
> Science Road
> Canberra
> ACT 0200
> Australia
>
> Phone: (02) 6125 8325
> Fax: (02) 6125 0750
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>

*****************************************************************
**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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