[gmx-users] water atom locations from genbox

Justin A. Lemkul jalemkul at vt.edu
Fri May 14 20:42:05 CEST 2010

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...



> thanks
> sikandar


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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