[gmx-users] Vacum minimizations and references

Dallas Warren dallas.warren at vcp.monash.edu.au
Wed Nov 20 03:03:28 CET 2002

>     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.

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy
Monash University
381 Royal Parade
Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9076
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