[gmx-users] Vacum minimizations and references

[K.A. Feenstra]

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
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|        | Anton Feenstra                                            |
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