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.moll...@ibs.fr
lucamollica...@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)
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
