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