Re: About ions Representation in NAMD

From: Gianluca Interlandi (
Date: Wed Sep 28 2005 - 07:33:39 CDT

Hi Yangbing,

If you use CHARMM PARAM27 the parameters and topology for Na and Cl are
already there. Unfortunately, the parameters for phosphate ions are
missing. I tried once to develop them myself per analogy but I was
unsuccessfull as they aggregated with Na ions building kind of stones. You
might need to do some quantum mechanical calculations to get it right.

Generally, I insert the ions manually and randomly into the pdb-file
containing water molecules and the protein already solvated. After that I
remove water molecules within 3 A distance from the ions. Also take care
that no ion is closer than 4-6 A to the protein in the starting
configuration. The total charge of the system must be neutral if you use
PME. I put as many ions to have roughly 150 mM concentration. Then I put
harmonic constraints to the atoms of the protein and run an equilibration
for 200 psec at constant temperature and pressure so that the water
molecules and the ions around the solute equilibrate and the water box
adjusts its volume. Finally, I release the constraints and run the
production using the restart file from equilibration.

I hope it helps, I don't know more.


On Wed, 28 Sep 2005 wrote:

> Hi All,
> I have a question about how to add ions to NAMD Smlaion systems as follows:
> There are always many types of ions in Biological Systems, such as calcium ions,
> sodium ions and phosphate groups. And there always exists interactions between
> these ions and Proteins, such as in Bone the binding of Hydroxyapatite to Collagen
> molecules is the fundamental functional structure and decides the basic property
> of Bone.
> So I want to know how to handle such ions in NAMD. Do I need to define all the
> topology files and force-field parameters by myself? And how it can be relized?
> Thank you!
> Your sincerely
> Yangbing

Gianluca Interlandi
                    +41 (0) 1 635 55 93
                    +41 (0)79 655 73 35

PhD-Student of the Department of Biochemistry
at the University of Zurich Irchel, Switzerland

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