Subject: SUMMARY: Approximate Water Treatment in MD

From: Gerald Loeffler <[email-masked]>
Date: Tue, 25 Feb 1997 13:45:24 -0800

Dear CCLers,

some time ago I asked "Which kind of approximate treatment of water in
MD-simulations of solvated systems have you used or do you know of?"

I'm very grateful to

	M.L.C.E. Kouwijzer,
	Michael Hartmann,
	Peter S. Shenkin,
	Fernando Luis Barroso da Silva,
	Tom Simonson

who took the time to answer to my question, and offered the following
solutions:

1) CHEAT95 is a force-field that implicitely includes solvent effects:
   a) M.L.C.E. Kouwijzer and P.D.J. Grootenhuis, J. Phys. Chem 99, 
      13426-13436 (1995).
   b) http://www.biosym.com/support/quanta/cheat95.html

2) Kowall et al. deal with MD simulations of the water exchange reaction
   of lanthanide ions:
   a) Kowall, Foglia, Helm and Merbach, Chem. Eur. J. (1996), 2,
      285-294

3) GB/SA is an implicit solvent model that is for instance implemented 
   in the Molecular Modelling package MacroModel
   (http://www.cc.columbia.edu/cu/chemistry/mmod/mmod.html):
   a) Hasel, W.; Hendrickson, T. F.; Still, W. C. , "A Rapid 
      Approximation to the Solvent Accessible Surface Areas of 
      Atoms",Tetrahedron Comput. Method. 1988, 1, 103.
   b) Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. , 
      "Semianalytical Treatment of Solvation for Molecular Mechanics and 
      Dynamics",J. Am. Chem. Soc. 1990, 112, 6127.
   c) Nagy, P. I.; Bitar, J.; Smith, D. A. ,"Comparison of the Solvent 
      Effect Calculated by the Generalized Born/Surface Area Method and 
      Monte Carlo Simulations",J. Comput. Chem. 1994, 15, 1228.
   d) Varnek, A. A.; Wipff, G.; Glebov, A. S.; Feil, D. , "An 
      application of the Miertus-Scrocco-Tomasi solvation model in 
      molecular mechanics and dynamics simulations",J. Comput. Chem. 
      1995, 16, 1.
   e) Reynolds, C. H. , "Estimating Lipophilicity Using the GB/SA 
      Continuum Solvation Model: A Direct Method fo Computing Partition 
      Coefficents",J. Chem. Inf. Comp. Sci. 1995, 35, 738.
   f) Urban, J. J.; von Tersch, R. L.; Famini, G. R. , "Effect of 
      Flourine Substitution on Phenol Acidities in the Gas Phase and in
      Aqueous Solution. A computational study using contiuum solvation 
      models.",J. Org. Chem. 1994, 59, 5239.
   g) Humphreys, D. D.; Friesner, R. A.; Berne, B. J. , "Simulated 
      Annealing of a Protein in a Contiuum Solvent by Multiple-Time-Step 
      Molecular Dynamics.",J. Phys. Chem. 1995, 99, 10674.

4) Smith and Pettitt published a paper on this subject:
   a) P.E.Smith and B.M.Pettitt, "Modeling Solvent in Biomolecular 
      Systems", J.Phys.Chem. 1994, 98, 9700-9711

5) G. Archontis, M. Karplus and T. Simonson have submitted a paper on a
   hybrid microscopic/continuum method for including long-range 
   interactions, where distant solvent is treated as a continuum, and 
   nearby solvent is treated microscopically.

Once again, I would like to thank all those who responded. There was
definitely some very valuable information contained in some of the
answers.

	Cheers,
	gerald
-- 

Gerald Loeffler
PostDoc in Theoretical Biochemistry

EMail: [email-masked]
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