[gmx-users] water atom locations from genbox

[Sikandar Mashayak]

suppose I am not going to use PBC and want all the atoms within the
specified boundaries..

On Fri, May 14, 2010 at 1:42 PM, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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