About the potential of NAMD

From: yangbing00_at_mails.tsinghua.edu.cn
Date: Thu Oct 06 2005 - 22:53:46 CDT

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

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!


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