[gmx-users] Box of water

[Mark Abraham]

On 1/05/2012 12:20 PM, cuong nguyen wrote:
> Thanks,
>
> 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.

Mark

> Cheers,
> Cuong
>
> 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
>
>     -- 
>     ========================================
>
>     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
>     <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
>
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> -- 
> Nguyen Van Cuong
> PhD student - Curtin University of Technology
> Mobile: (+61) 452213981
>
>
>

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