[gmx-users] Box of water
Mark.Abraham at anu.edu.au
Tue May 1 04:23:49 CEST 2012
On 1/05/2012 12:20 PM, cuong nguyen wrote:
> I tried to add -maxsol 846 to the command and got the box with 846
> water molecules. However, when I use VMD to visualize the box, these
> molecules concentrate on 1/3 the box space. I do need the molecules to
> spread out whole box.
So next time think about asking the question whose answer you actually
want... Do some arithmetic and put a suitable box around a single water
molecule. Then replicate with genconf, like I suggested last time.
> 2012/5/1 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> On 4/30/12 10:02 PM, cuong nguyen wrote:
> Dear Gromacs Users,
> I used the command "genbox -cs spc216.gro -o box1.g96 -p
> topol.top -box 3 3 10"
> to create box of 3010 water molecules. However, now I need to
> create a same size
> box with only 846 water molecules. Please help me to do this.
> Use the -maxsol option when invoking genbox.
> 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
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> Nguyen Van Cuong
> PhD student - Curtin University of Technology
> Mobile: (+61) 452213981
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