[gmx-users] water atom locations from genbox
symashayak at gmail.com
Fri May 14 20:48:11 CEST 2010
suppose I am not going to use PBC and want all the atoms within the
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
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
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> jalemkul[at]vt.edu | (540) 231-9080
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