[gmx-users] Concentration

Chih-Ying Lin chihying2008 at gmail.com
Wed Nov 26 22:00:54 CET 2008

How to make a solution with specific concentration ?

Command 1 =>
editconf -d  0.75  -bt cubic
0.75=Distance between the solute and the box
cubic = the type of the simulation box

Command 2 =>
genbox -cp solute.gro -cs spc.gro -box Y Y Y
Y = the box vector in nm

If I use cubic in my system, is Y defined as the length of the cubic in the
three directions?
Is the overall volume of the simulation box = Y * Y *Y  (nm*nm*nm) ?
Is the center of cubic on the origin (0,0,0) of the coordinate?

Thank you
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