[gmx-users] Gromacs inquiries

cuong nguyen nvcuong68 at gmail.com
Wed Oct 26 08:18:03 CEST 2011

Dear Mark,

I used to put ten molecules of hexanol in a box 5 5 1 with the instruction
"genbox -ci hexanol.gro -nmol 10 -box 5 5 1 -o layer.gro -p hexanol.top".
However, now I want to fill up the box 4 4 4 with hexanol molecules.
If I change the number 10 in the instruction to 1000 or 10000, it will run
well but I do not know if this box is full.
Please help me to change this instruction.

Thanks a lot.



2011/10/26 Mark Abraham <Mark.Abraham at anu.edu.au>

> On 26/10/2011 1:46 PM, cuong nguyen wrote:
>> Dear,
>> Thanks a lot for useful software. I am trying to generate a box (4 4 4)
>> with full hexanol molecules inside. I have used the instruction "genbox -ci
>> hexanol.GRO -box 4 4 4 -o layer.gro -p hexanol.top", however it has not been
>> successful.
> Unfortunately we can't help if we don't know what is in your -ci box (also,
> it's probably best not to use capitalized filename extensions), or why you
> think the procedure was not successful. Please consider the advice here
> http://www.gromacs.org/Support**.
> Mark
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Nguyen Van Cuong
PhD student - Curtin University of Technology
Mobile: (+61) 452213981
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