[gmx-users] Force fields, is there a review article?
David van der Spoel
spoel at xray.bmc.uu.se
Sun Aug 26 08:50:15 CEST 2012
On 2012-08-25 13:07, Luca Mollica wrote:
>> 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
>> 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
>> 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:
> 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:
> like many papers written by Raphael Bruschweiler (like this:
> 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):
> 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.
We have done a couple of evaluations recently
Erik Marklund, Daniel Larsson, Alexandra Patriksson, David van der Spoel
& Carl Caleman: Structural stability of electrosprayed proteins:
temperature and hydration effects Phys. Chem. Chem. Phys. 11 pp.
8069-8078 (2009) http://dx.doi.org/10.1039/b903846a
Carl Caleman, Paul J. van Maaren, Minyan Hong, Jochen S. Hub, Luciano T.
Costa, David van der Spoel: Force Field Benchmark of Organic Liquids:
Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension,
Compressibility, Expansion Coefficient and Dielectric Constant J. Chem.
Theor. Comput. 8 pp. 61-74 (2012)
Oliver Lange, David van der Spoel and Bert de Groot: Scrutinizing
Molecular Mechanics Force Fields on the Microsecond Timescale With NMR
Data Biophys. J. 99 pp. 647-655 (2010)
>> I search through abstracts in molecular dynamics at the library, but I
>> 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
>> 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):
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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