From: zoran (
Date: Sat Dec 13 2014 - 17:22:16 CST

Well, this is good sign that something of my trouble touch others.
Axel wrote: “if you knew a bit more about force fields and the chemistry of
transition metals, you wouldn't make such a general attack”
I really now a bit about force fields and think more about TM chemistry. I already stated in my earlier posts that I am novice in this parameterization processes. So You have to be really rigorous scientist to describe my sentence: I am very sorry that scientists...forget...,
as a attack of a “know-nothing” person. One may, if he/she wants to, draw conclusion that my statement was request for help in this field and in no way general attack (what a word) on people doing FF-MD theory.
Thanks for critical discussion Francesco.

While I obviously agree with Axel about the basic science illustrated, there are situations where such dirty parameterizations of transition metal clusters for classical MD prove useful. That is the case when the focus is not the metal complex, while conservation of the geometry of the metal complex during MD is what matters. A case in point is PNAS ͉ August 14, 2007 ͉ vol. 104 ͉ no. 33 ͉ 13319 –13324 If you read the PhD thesis behind that, you see that that work was carried out with those limitations in mind. In my view it proved useful. Consequently, tools to develop params for tm complexes may have their interest. Such as the MCPB toolkit in amber quarters, if it goes beyond Zn. cheers francesco pietra

On Sat, Dec 13, 2014 at 10:15 PM, Axel Kohlmeyer <> wrote:
  can't let this go uncommented...

  On Sat, Dec 13, 2014 at 7:50 AM, zoran <> wrote:


> I am very sorry that scientists making force fields for macromolecules
> forget on transition metals (in general) and that TM make a substantial part
> of biological processes.

  if you knew a bit more about force fields and the chemistry of
  transition metals, you wouldn't make such a general attack. people
  don't do parameters for transition metals for classical (pairwise
  additive) force fields, because it is pretty damn near impossible to
  get them right. already divalent cations are a big stretch in most
  cases and rarely represented well. force fields are always a
  compromise, but in the case of transition metals, you have to deal
  with the problem of having to describe interactions that have
  substantial directional and manybody character (i.e. the interaction
  of the transition metal depends on how many and what neighbors are
  where) with a spherical functional form. of course, you can follow the
  recipe for force fields and derive some parameters, but in most cases,
  the resulting simulations are a waste of time. considering the fact
  that many force field users are very uncritical about how to use
  parameterizations, it is quite understandable, that people, who
  specialize in force field parameters, do not want to lead people down
  that road and rather not generate and publish sub-standard parameters.

  if you know a way how to do these parameterizations so they are
  producing meaningful calculations, please don't hold back and let us
  know. we most certainly do not need people that blame everybody else
  but themselves.


> With my best regards to all of you
> Zoran

  Dr. Axel Kohlmeyer
  College of Science & Technology, Temple University, Philadelphia PA, USA
  International Centre for Theoretical Physics, Trieste. Italy.