CCL: A review of force fields

["Fiona Case" <fhcase(a)hotmail.com>]

 Sent to CCL by: "Fiona Case" [fhcase###hotmail.com]
 Hello,
I'd like to suggest that you have two questions to answer: Which
 forcefield
 to use, and which method to use (MD/MC, which flavor?). If you make a
 wise
 choice of forcefield, but a poor choice of method, you will still get
 poor
 results.
Also, when you look at many of the "forcefield review"
 papers they consider
 intramolecular interactions (bond lengths, bond angles, vibrational
 frequencies obtained from isolated molecules, etc.). Unless you are
 trying
 to predict properties of molecules in a vacuum, intermolecular
 interations
 are at least as important. Most do not consider the effect of
 temperature or
 pressure, nor do they provide guidence on the transferability of the
 forcefields (what will happen if your molecule is slightly different to
 the
 one used in the published study?)
This lack of validation/verification/guidence has been identified as a
 major
 limitation to the useful application of force field based methods.
 http://www.chemicalvision2020.org/pdfs/compchem.pdf
 http://fluidproperties.org/Vision-and-Strategic-Plan-5-Feb-06.pdf
However, there is some good news: Some organizations are attempting to
 solve
 this problem. If you take a look at the publications and websites that
 have
 resulted from their efforts you will already see some guidence on
 forcefield
 and method selection for "useful" simulations.
1) The Industrial Fluid Properties Simulation Collective (of which I
 am a
 member)http://fluidproperties.org/
 2) The BioSimGrid, http://www.biosimgrid.org/
 3) The protein folding challenges: http://predictioncenter.org/
4) If you are looking at something that is a crystal, see the Crystal
 Structure Prediction challenges:
 http://scripts.iucr.org/cgi-bin/paper?S0108768105016563
You could encourage every "modeling expert" you meet
 (particularly in
 academia) to support these efforts. The problems you are facing in
 trying to
 select a forcefield and method to use for your work are shared by
 everyone
 attempting to apply these methods. It is of benefit to us all that more
 validation/verification/guidence becomes available so that molecular
 simulations methods become "useful" to the wider world, and
 particularly in
 industry.
 Fiona Case
 ----Original Message Follows----
>  From: "Carlos Nunez carlos_javierna*o*yahoo.com"
>  <owner-chemistry#ccl.net>
 Reply-To: "CCL Subscribers" <chemistry#ccl.net>
 To: "Case, Fiona " <fhcase#hotmail.com>
 Subject: CCL: A review of force fields
 Date: Thu, 16 Mar 2006 20:57:41 -0500
 Sent to CCL by: "Carlos  Nunez" [carlos_javierna{:}yahoo.com]
 Hi,
 See this:
 MacKerell A. D. Jr. 2004. Empirical force fields for biological
 macromolecules: overview and issues. J. Comput. Chem. 25: 1584-1604.
 Hasta la proxima vez,
 Carlos N.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp-:-//www.ccl.net/chemistry/sub_unsub.shtmlhttp-:-//www.ccl.net/spammers.txt