[gmx-users] Gromacs inquiries

[Mark Abraham]

On 26/10/2011 5:18 PM, cuong nguyen wrote:
> 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.

It probably can't be full. genbox -ci does not generate a close packing, 
so the first part of your procedure isn't useful, as you would have 
learned from reading genbox -h. See 
http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation for a 
sound workflow.

Mark

>
> Thanks a lot.
>
> Regards,
>
> Cuong
>
> 2011/10/26 Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto: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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