On 08/28/09, tekle...@ualberta.ca wrote: > > Hi Justin, > > "There is something physically unrealistic about your model" > > You are right! > > The main problem I found out is that some of the structures in my Solution > broke down...... > > I used ... > > genbox -cp XXXX.grob -nmol 20 -ci insert.gro -cs spc216.gro XXX.top > -XXXXXX.gro > > To generate multiple structures in a box. However, it creates overlap and my > orginal structures broke down. I checked the structures! > > Can you please let me how to generate multiple structures in a fixed box at > random or packed in a solutio (e.g water) > No, because that's not a well-defined proposition. You could generate a small box with one solute +solvent, and then use genbox to replicate it. Then when random velocities are generated and you equilibrate you will achieve the same effect you describe.
Mark
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