[gmx-users] Re Multiple Chains

[Justin A. Lemkul]

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.

-Justin

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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