[gmx-users] gromacs use

[Anton Feenstra]

CORINA BARBU wrote:
>  Hello!
> 
> My name is Corina Barbu and I'm looking for a code useful to do Molecular
> Dynamics on a ~150 atoms organic molecule. I have a synthetic molecular motor
> made of very many benzene rings(and some other atoms as:O,N,S and Si). As far
> as I know GROMACS is made for biomolecules(as far as the implemented force
> fields are concerned). I was still thinking if it still worth it to try it. I
> wonder in what extent is suitable for my system. Maybe you have suggestions for
> some other codes also (I need a combination of a MM force field and possibility
> of doing MD in the presence of an external electric field).
> Thank you very much! Corina 

Sounds like a perfect job for Gromacs. The most difficult part, on your side,
would be to build the topology for your system. You can use the ProDrg server
to get a good starting point. If you will be using the 'old' Gromacs forcefield
(ffgmx), you'r nearly done, but I'd reccomment using either the Gromos ff
(ffG43a) or OPLS since these incorporate mayor improvements over the 'old' ffgmx.


-- 
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)                               |
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