[gmx-users] Gromacs inquiries

[Justin A. Lemkul]

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.
> 

You can find out whether your box is full in several ways.  The first, and most 
direct, method is to open the new coordinate file in the visualization software 
of your choice and see if the molecules fill the box.  If there are voids, then 
add more.  The other option is to set a very high value of molecules to be 
added, and genbox will add until it cannot any more.  The latter method may be 
somewhat time-consuming, so choose a sensible value, even if it is higher than 
what you may want (e.g., try 5000 instead of 5000000).

-Justin

> 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
>  
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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