mark.abraham at anu.edu.au
Sun Aug 30 11:47:23 CEST 2009
On 08/28/09, teklebrh at 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.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users