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
--
========================================
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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