[gmx-users] Vacum minimizations and references
K.A. Feenstra
Feenstra at chem.vu.nl
Wed Nov 20 08:15:21 CET 2002
Dallas Warren wrote:
>> I would like to know how should I proceed to perform a energy
>> minimization of a protein in vacuum instead of a water's box. Is it
>> possible in GROMACS ?
>
>
> Simple do not add the water molecules/solvent to the box.
>
> Something as complex and large as a protein might do some unusual things
> without the water present though (I don't deal with proteins, so don't
> know for sure). I suppose it depends on the reason for wanting to do
> the energy minimisation without water present.
Energy minimization in vacuum is relatively safe. Most deviations will
occur at the surface sidechains, but I have not usually seen large
changes even there. (Dynamics in vacuum is a different matter, though.)
As for literature, I think there is a list of Gromacs related papers on
the website (http://www.gromacs.org), or else check out the Alan Mark
MD-group homepage at the University of Groningen (http://mdgroup.chem.rug.nl),
under 'Articles'. There you can also find a link to the Van Gunsteren
group at the ETH in Zuerich, where the Gromos software and forcefield are
developed.
--
Groetjes,
Anton
________ ___________________________________________________________
| | Anton Feenstra |
| . | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
| |---- | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands |
| |---- | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| ' __ | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
| / \ |-----------------------------------------------------------|
| ( ) | Dept. of Biophysical Chemistry - University of Groningen |
| \__/ | Nijenborgh 4 - 9747 AG Groningen - The Netherlands |
| __ | Tel +31 50 363 4327 - Fax +31 50 363 4800 |
| / \ | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton |
| ( ) |-----------------------------------------------------------|
| \__/ | "If You See Me Getting High, Knock Me Down" |
| | (Red Hot Chili Peppers) |
|________|___________________________________________________________|
More information about the gromacs.org_gmx-users
mailing list