[gmx-users] Re: Inquiry Again.

[Anton Feenstra]

Victor Kowalenko wrote:
> I was a little the pdb2gmx might be restricted to only molcular
> applications. Your option of adjusting the topology file manually
> might be superior. Again I will look into this on Monday.

 From your description, it sounds as if you may only need Lennard-Jones
potential interactions, in which case it is fairly trivial to write the
Gromacs topology with your parameters. If you need bonded interactions
(that is, e.g. harmonic bond-stretching potential on two atoms or harmonic
angle-bending on three (bonded) atoms), you will probably also be better
off by generating this topology yourself with e.g. a script. In either
case pdb2gmx probably isn't helpful since it was designed for (bio-)
polymer-like molecules. I know of someone at Theoretical Chemistry in
Groningen (Netherlands) who simulated NaCl crystals in Gromacs, although
I don't remember if he had bonds.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|