Re: About the potential of NAMD

From: Brian Bennion (
Date: Fri Oct 07 2005 - 10:35:42 CDT

If I understand this question right you say that using the bonded
potentials to describe free ions is incorrect, and you would be right.

However you do not understand the nonbonded portion of the force field.
It is the Van Der Waals and electrostatics
that govern free ions, not the bonded terms.

I dare say that there are at least 20 or more potentials out there that
people could implement into NAMD. I have even tried this myself with the
ZPL potential. Most of these potentials deal with states of matter not
usually seen the the biological arena and therefore are not "harmonic" in
dealing with bonded interactions or infinite crystaline materials.

People use ions in charmm/namd driven simulations all the time.
Please read the documentation to better understand the force field in
classical MD.


 On Fri, 7 Oct 2005 wrote:

> Hi All:
> Another related question:
> NAMD is based on the CHARMM potential which adopts the Harmonic Assumption. As we
> all know, Harmonic assumption will be a good compromise to investigate the big
> biological molecule, 'cause this assumption make the Potential and the Force more
> easily achieved. And a CHARMM force parameter file will be convenient to be
> adopted.
> However, there existed sereval kinds of different potential in Solid Physics, such
> as Embedded Atom Potential, Tight Band Potential, and so on. Also must be
> highlighted is the Tersoff and Berner Potential for Carbon and Silicon. The major
> character of these potential is that there exist a minimum of potential VS
> distance. These potantial could accuractely describe the near-equilibrium state,
> and decrease to zero as the distance increases to infinite, which is consistent
> with the theory. However, this is not the case for CHARMM potential. There also
> existed a minimum of potential VS distance, but as the distance increases to
> infinite the potential also increases to infinite. CHARMM potential is accurate
> just for the both sides of very near equilibrium, and so is just convenient for
> That means that two atoms can not be very far from each other, which would be OK
> for biological system 'cause bond is the most important. However, we can consider
> another biological system, that includes various ions and proteins, such as bone
> (calcium phosphate and collagen). Ions play a critical rule in these systems and
> the detail mechanism is still unknown. Such systems have been an active research
> area named as Biomaterials and Tissue Engineering. The question is that can NAMD
> be convenient for these systems? Unfortunately, the answer would be NO, 'cause for
> the ions we could not adopt the Harmonic Assumption anymore. Just consider when
> the concention is low, ions can be very far from each other, and the bond
> description (harmonic assumption) is never OK for ions.
> Harmonic assumption also restricts the investigation on some other characters
> related with Unharnomic Items of the potential, such as Phonon effect,
> ferroelectric and so on.
> A possible solution would be to adopt sereval more accurate potential to replace
> the Harmonic Assumption, which could describe the Ions conveniently. However,
> there will be many difficulities, 'cause new potential will change the normal
> structure of NAND, such as change the form of CHARMM forcefield parameter file
> (make it more complicated than the Harmonic Assumption)
> So have anynone considered developing the NAMD for these ions-included systems? Or
> do the developers of NAMD have such plans? Can you give some instructions on the
> introduction of new potantial form?
> If anyone is interested, in-depth discussions is particularly welcomed!
> Thank you!
> Yangbing

  Brian Bennion, Ph.D.
  Bioscience Directorate
  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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