VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Dec 13 2014 - 15:15:52 CST

can't let this go uncommented...

On Sat, Dec 13, 2014 at 7:50 AM, zoran <zmatovic_at_kg.ac.rs> 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.

axel.

> With my best regards to all of you
> Zoran
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.