[gmx-users] Ice box

David spoel at xray.bmc.uu.se
Mon Oct 10 19:28:32 CEST 2005

On Tue, 2005-10-11 at 02:31 +1000, Mark Abraham wrote:
> Fernando Mattio wrote:
> > Dear gromacs users,
> > I would like to know if it is possible with gromacs to create a box not 
> > with water and protein, but only with ice. I couldn´t generate a 
> > topology of the ice in the prodrg sever, and the command pdb2gmx didn´t 
> > work... So I am wondering if it is possible...
> Find an X-ray diffraction paper that determined the crystal structure, 
> and use that to build an algorithm to generate an ice structure. That 
> would create "ideal" ice, but inevitably real ice has imperfections 
> because the cooling process was not infinitely slow and the crystal 
> growth was thus seeded.


  author =       {J. A. Hayward and J. R. Reimers},
  title =        {Unit cells for the simulation of hexagonal ice},
  journal =      {J. Chem. Phys.},
  year =         1997,
  volume =       106,
  pages =        {1518-1529}

> My guess is that it is close to vanishingly unlikely that a 
> general-purpose forcefield for a multi-center water molecule would 
> actually model the behaviour of crystalline water accurately, much less 
> the density expansion below 277K. Thus getting a box of water and 
> cooling it to 273K slowly isn't likely to work.
> pdb2gmx will only have a chance of working if you can generate an ice 
> coordinate file some other way.
> Mark Abraham
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David van der Spoel, PhD, Assoc. 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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