[gmx-users] How to avoid centering of solute by genbox

Dallas B. Warren Dallas.Warren at vcp.monash.edu.au
Tue May 29 23:59:08 CEST 2007

>I am trying to solvate a protein in a rectangular box, keeping it
towards one face.
>But whatever position I choose ( with editconf - translate ), genbox is
centering it
>while solvation. How to override this and keep the protein not at
center of box? 

Why is this a concern?

For simulation purposes, because of PBC, it doesn't matter where in the
box the protein is located.

For visualisation purposes, that is something that you deal with after
the simulation has been run.

Catch ya,

Dr. Dallas Warren
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 9524
When the only tool you own is a hammer, every problem begins to resemble
a nail.

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