[gmx-users] Box size

Dallas Warren dallas.warren at vcp.monash.edu.au
Thu Nov 4 00:48:37 CET 2004

>   Now my system is well equilibrated by evaluating density and energy 
> parameters, however the box size (2.87931, 4.02635, 5.40494) is not what 
> we want, we would like to have a cubic shape instead. I thought about 
> setting the box size to 5.40494 in three dimensions, which means starting 
> the whole equilibrium again and may take very long simulation time. Is 
> there any other efficient way to fulfill that in Gromacs?

Are you using anisotropic pressure coupling?  If you want to maintain a 
cubic shape, and it wont interfere with the manner in which the system 
behaves change it to isotropic.

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 9083
When the only tool you own is a hammer, every problem begins to resemble a nail.
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