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

From: Brian Bennion (
Date: Tue Mar 16 2004 - 13:07:07 CST

I read the same email message on ccl.

I have thought about this problem as well and have tested systems both

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.


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 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 **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **

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