[gmx-users] How to generate the initial coordinates file?

[Justin A. Lemkul]

On 5/29/12 8:46 AM, Bao Kai wrote:
> Hi,  all,
>
> I am new to Gromacs and MD.  I just went through a few tutorials on
> Gromacs quickly.  I have a question now.
>
> I know the structure of molecule A and B, such as the atoms
> compositions and the relative position of the atoms and the charge.
>
> Now, I want to use 500 A and 100 B to do the simulation. I want to
> know how I can get the initial coordinate file or how I should start.
>
> It seems all the tutorials use either one big protein molecule the add
> some water or the coordinate files have been ready.
>
> Thank you very much.

You will need to obtain coordinate files of both of your molecules using some 
external software.  Several suggestions are provided here, though there are 
others, as well:

http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources

You will need to obtain or create topologies for each of these.

To construct the system, use genbox in conjunction with the -ci -nmol flags, as 
suggested here:

http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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