[gmx-users] Solvent parametrization protocol
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,
Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
mailto:baaden at smplinux.de - ICQ# 11466242 - http://www.marc-baaden.de
FAX/Voice +49 697912 39550 - Tel: +44 1865 275380 or +33 609 843217
More information about the gromacs.org_gmx-users