VMD-L Mailing List

From: zoran (zmatovic_at_kg.ac.rs)
Date: Sat Dec 13 2014 - 18:54:35 CST

have it whatever way you want. i personally find it is a rather
unusual approach to ask for help by overtly antagonizing people.
but if you believe that this is the way that things should work, don't
let me stop you.

I do not know what are you talking about really but I feel the need to
answer you and that will be my last: I don't remember when I was last time
offensive toward others - it is not my style - and therefore I behaved the
same in my post about fftk.
Major part of my research I am doing in experimental chemistry and try to
give my best to complete it with computational chemistry.

And you know what, may be looks like a joke for you, but I'll see what I can
do with a gap between classical ff and TM.

with my best regards
zoran

    axel.

>
> Thanks for critical discussion Francesco.
>
> ZDM
>
> 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 <akohlmey_at_gmail.com>
> wrote:
>>
>> 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.
>>
> 

-- 
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.