Sikandar Mashayak wrote:
suppose I am not going to use PBC and want all the atoms within the
specified boundaries..
Then either change your box size to make it slightly larger (and since you're
using -maxsol, it won't change the number of molecules), or change the value of
-seed when running genbox to get a different configuration until you've got one
that you're satisfied with.
-Justin
On Fri, May 14, 2010 at 1:42 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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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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