[gmx-users] water atom locations from genbox

[Justin A. Lemkul]

Sikandar Mashayak wrote:
> I have to create a box with given number of water molecules (spc/e) in 
> it.  So I use genbox -cs spc216.gro -maxsol n -box , with appropriate 
> box size and n.
> But I observe in the out.gro that some atoms are outside the box, so How 
> do I make genbox to keep all atoms within the box specified?
> 

If you plan on using periodic boundary conditions, "outside" is irrelevant...

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin

> thanks
> sikandar
> 

-- 
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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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