[gmx-users] Re Multiple Chains

Justin A. Lemkul jalemkul at vt.edu
Thu Sep 16 04:37:39 CEST 2010

C Johnson wrote:
> """
> Note that the genbox box stacking you are using here is not necessarily
> what you want.  What sort of starting configuration do you want?  Is the
> concentration / spacing that you get when you stack boxes like that,
> actually what you want?  Or do you want a more concentrated type of
> system where the molecules are intertwined etc.?
> Catch ya,
> Dr. Dallas Warren
> """
> It would be cool if I could change the starting configuration but right 
> now I'm just happy that the simulation worked (Thanks both you and 
> Justin for the help).
> Do you have any tips/walkthroughs on how to adjust the starting 
> configuration?

You can apply random rotations with genconf -maxrot, insert molecules randomly 
in a box with genbox -ci -nmol, or specifically place molecules using editconf 
-center on each one of them, then concatenate the resulting file.

Unfortunately there aren't tutorials for all things.  Reading the documentation 
and doing some experimentation will serve you well.


> I'm a synthetic chemist but have had an interest in simulation for 
> awhile so I appreciate the help.
> Casey


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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