[gmx-users] water atom locations from genbox

[Justin A. Lemkul]

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 <jalemkul at vt.edu 
> <mailto:jalemkul at 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

========================================