[gmx-users] Solvent parametrization protocol

Marc Baaden baaden at smplinux.de
Wed Aug 7 11:44:21 CEST 2002


thanks for all the comments about water. The reason why I am interested in
this, is that I am working on a model for an organic solvent that I would
at some point like to combine in a mixed box with water.

Now I was wondering whether there is any 'best protocol' for parametrising
a solvent and/or any tools to do it.

My solvent only has 5 atom types based on P, OM, OS, CH2 and CH3 and I
would like to use it with PME, Nose-Hoover Tcoupl and Raman-Parrinello

As a general approach I guess this is fairly standard:
- Bonded terms are quite straight forward from structural data.
- Charges should reproduce the dipole moment.
- Lennard-Jones is fine-tuned for density, heat of vaporization

Now one thing I wonder is, should I eg touch the CH2/CH3 LJ parameters ?
As these are supposed to be transferable ?

If the dielectric calculated from the model is a bit off, should one
play with the charges ?

Also, is there a preferred order for varying the parameters ? And evtl.
any "g_parametrise" to do so ?

Thanks in advance,
  Marc Baaden

 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
 mailto:baaden at smplinux.de  - ICQ# 11466242 -  http://www.marc-baaden.de
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