[gmx-users] Force Fields and Electrostatics

[David van der Spoel]

On Thu, 2004-04-01 at 22:59, Dallas Warren wrote:
> David,
> 
> Thank you for the reply, much appreciated.
> 
> Is there anyone else out there that had simulated the same system using different treatment of the electrostatics?  And find a difference, or not?
> 
there's zillions of such papers... check literature for
cut-off artefact simulation
@Article{Steinhauser92,
  author = 	 {O. Steinhauser and H. Schreiber},
  title = 	 {Taming cut-off induced artifacts in molecular
                  dynamics studies of solvated polypeptides, the
                  reaction field method},
  journal = 	 BTjmb,
  year = 	 1992,
  volume =	 228,
  pages =	 {909-923}
}
@Article{Chipot94,
  author = 	 {C. Chipot and C. Milot and B. Maigret and P. A. Kollman},
  title = 	 {Molecular dynamics free energy simulations:
                  Influence of the truncation of lang-range nonbonded
                  electrostatic interactions on free energy
                  calculations of polar molecules},
  journal = 	 BTjcp,
  year = 	 1994,
  volume =	 101,
  pages =	 {7953-7962}
}
@Article{Fox96a,
  author = 	 {T. Fox and P. A. Kollman},
  title = 	 {The Application of Different Solvation and Electrostatics
Models in  Molecular Dynamics Simulations of Ubiquitin: How Well is the
{X}-{R}ay Structure "Maintained"},
  journal = 	 BTprot,
  year = 	 1996,
  volume =	 25,
  pages =	 {315:334}
}
@Article{Aqvist99a,
  author = 	 {J. {\AA}qvist},
  title = 	 {Long-range electrostatic effects on protein folding},
  journal = 	 BTfebs,
  year = 	 1999,
  volume =	 457,
  pages =	 {414-418}
}
@ARTICLE{Zuegg99a,
	author	    = {J. Zuegg and J. E. Greedy},
	title	    = {Molecular dynamics simulations of human prion protein:
	  Importance of correct treatment of electrostatic interactions},
	journal     = {Biochemistry},
	year	    = {1999},
	volume	    = {38},
	pages	    = {13862-13876}
}
@Article{Walser2001a,
  author = 	 {R. Walser and P. H. Hunenberger and W. F. van Gunsteren},
  title = 	 {Comparison of different schemes to treat long-range
electrostatic interactions in molecular dynamics simulations of a
protein crystal},
  journal = 	 {Proteins},
  year = 	 2001,
  volume =	 43,
  OPTnumber =	 4,
  pages =	 {509-19},
  month =	 {Jun.}
}
@Article{Patra2003a,
  author = 	 {M. Patra and M. Karttunen and M. T. Hyvonen and E. Falck
and P. Lindqvist and I. Vattulainen},
  title = 	 {Molecular dynamics simulations of lipid bilayers: major
artifacts due to truncating electrostatic interactions},
  journal = 	 {Biophys. J.},
  year = 	 2003,
  volume = 	 84,
  pages = 	 {3636-3645}
}

@Article{Spoel98a,
  author	= {D. van der Spoel and P. J. van Maaren and H. J. C.
		  Berendsen},
  title		= {A systematic study of water models for molecular
		  simulation},
  year		= 1998,
  journal       = BTjcp,
  volume        = 108,
  pages         = {10220-10230}
}


And so on....


> Catch ya,
> Dallas Warren
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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