[gmx-users] Re: xtal-water

David van der Spoel spoel at xray.bmc.uu.se
Sat Mar 16 11:53:33 CET 2002

On Fri, 15 Mar 2002 nesanfor at criba.edu.ar wrote:

>Dear Mr. van del Spoel
>    Excuse me to answer this mail by an outer paht from le gmx list but my 
>question - appealing to your kindess - is beyond the subject of biomolecular 
>simulation. I was quite surprised by your assertion about the spc model as I 
>always understood that the spce featured an improvement of spc (diffusion 
>constant, dielectric constant, density, and an acceptable agreement in the O-O 
>distribution). I would appreciate if you can enlight me with some references 
>that point out the spc model as the recommended for solvation in biomolecular 
The point with SPC/E is that it may be overpolarised, excellent for bulk,
but not so good for interfaces. Check out these refs:

  author =	 "A. R. van Buuren and S. J. Marrink and
                  H. J. C. Berendsen",
  title =	 "A Molecular Dynamics Study of the Decane/Water
  journal =	 {J. Phys. Chem.},
  year =	 "1993",
  volume =	 "97",
  pages =	 "9206--9212",

  author = 	 {D. P. Tieleman and H. J. C. Berendsen},
  title = 	 {Molecular Dynamics Simulations of a fully hydrated
                  dipalmitoylphosphatidylcholine bilayer with
                  different macroscopic conditions and parameters},
  journal = 	 {J. Chem. Phys.},
  year = 	 1996,
  volume =	 105,
  pages =	 {4871--4880}

  author = 	 "David van der Spoel and Aldert R.  van Buuren and
		  D.  Peter Tieleman and Herman J. C.  Berendsen",
  title = 	 "Molecular Dynamics Simulations of Peptides from
                  {BPTI}: A Closer Look at Amide-Aromatic
  year =         1996,
  journal =      {J. Biomol. NMR},
  volume =        8,
  pages =       {229-238}

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

  author = 	 {P. Mark and L. Nilsson},
  title = 	 {Molecular dynamics simulations of the Ala-Pro dipeptide in water: Conformational dynamics of trans and cis isomers using different water models},
  journal = 	 {J. Phys. Chem. B},
  year = 	 2001,
  volume =	 105,
  pages =	 {8028-8035}

  author = 	 {P. Mark and L. Nilsson},
  title = 	 {Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K},
  journal = 	 {J. Phys. Chem. A},
  year = 	 2001,
  volume =	 105,
  pages =	 {9954-9960}

>Thank you in advance...
>yours truly

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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