[gmx-users] LINCS

[Mark Abraham]

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.

Mark


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090830/7199bb2d/attachment.html>