[gmx-users] How can I reconstruct the system in CGMD simulation?

Mark Abraham Mark.Abraham at anu.edu.au
Thu Dec 17 13:42:23 CET 2009

rasoul nasiri wrote:
> greetings GMX users,
> When I use genbox command for filling solvent in CGMD simulation with 
> Gromacs suit, I must use a larger van der Waals distance to avoid 
> crashes. when I use default value (0.105nm), system will crash. Which 
> distance is suitable for performing CGMD simulation. I used  0.15 or 
> 0.2nm as distances. Are those OK? 

Read up on your forcefield and find out how "large" the particles tend 
to be. It only has to be good enough, not perfect.

> I have to switch back to the smaller 
> radius afterward, Is it correct? 

Changing what for what purpose?

> if yes, How can I do it? I tried with 
> editconf but could not.

I don't know what you mean.


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