[gmx-users] Force fields, is there a review article?

[Luca Mollica]

> I have read a variation on this advice many. many times here:
>
> "The ultimate choice of force field should be based on your reading and
> understanding of their derivation and known applications/limitations, all of
> which comes from the literature.  Choose the one that you think is most
> sound :)"
>
> I am probably not the only person here who is attempting to learn and use
> molecular dynamics software for the first time.  I am probably not the only
> person here who is trying to simulate a molecule for which there is NO
> published molecular dynamics study.  Sure, it's a protein in water.  Is that
> enough to tell me which force field(s) will give me a representative result,
> or not?

maybe one of the best thing to do is to test the FF vs experimental data 
and check which one reproduces them better or provides more stability.
a recent example, a bit oriented toward a particular field of research 
but interested in terms of methodology used is the following one by 
David Case:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2997720/.

this sentence explains you why:"The high resolution of the diffraction 
data (0.96Å) and the simplicity of the crystallization solution (nearly 
pure water) makes it possible to attribute any inconsistencies between 
the crystal structure and our simulations to artifacts of the models 
rather than inadequate representation of the crystal environment or 
uncertainty in the experiment.".
it's not a problem of how it sounds, but if it "works" in sense of 
reproducing exprimental data, indeed.
being a person that works in the world of NMR, I am always interested in 
FF that are tested against experimental data in my field, so this paper 
is interesting too:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905107/?tool=pmcentrez.

like many papers written by Raphael Bruschweiler (like this: 
http://spin.magnet.fsu.edu/pubs/li_g28-g8_jctc2011.pdf).
this one is relevant for AMBER FF lovers (like me) but also because it 
enters a bit in depth in the details of the delicate but necessary 
operation of improving a FF (a thing we experimentalists that use MD 
always have to trust but, I think, with a careful and critical eye kept 
on the problem):

http://www.ncbi.nlm.nih.gov/pubmed/16981200.

water is crytical too, a bit is written in the David Case paper I have 
cited but even more can be found in literature (I am not an expert in 
this topics).
maybe someone else in the ML can be more helpful than me about this.


>
> I search through abstracts in molecular dynamics at the library, but I never
> seem to find articles which are general enough.  It would be very helpful if
> someone more knowledgeable in the field could point us newcomers at a review
> article, even a somewhat dated one, which surveys the use and utility of a
> few different force fields.  It would be a good starting point.

this one seems to be a thing of the kind you are looking for, but I 
don't know it even though it seems interesting (just found googling the 
title of other papers I have just listed):

http://maxwell.uncc.edu/abaumket/phys6203_files/Reading/force-fields.pdf

Regards.

L






-- 
Luca Mollica
Protein Dynamics and Flexibility by NMR
Institut de Biologie Structurale "Jean-Pierre Ebel"
UMR 5075 CNRS/CEA/UJF
41 rue Jules Horowitz
38027 Grenoble Cedex 01

E-mail:   luca.mollica at ibs.fr
           lucamollica.lm at gmail.com
Skype:    lucamollica
Linkedin: http://fr.linkedin.com/in/lucamollica

Tel: +33.(0)438783889
Fax: +33.(0)438785494

We need not destroy the past. It is gone.
(J.Cage)