[gmx-users] (no subject)

Mark Abraham Mark.Abraham at anu.edu.au
Fri May 8 12:26:42 CEST 2009

Antonia V. wrote:

Please use a descriptive subject line and reply quoting the previous 
message. It's not your reader's job to work out your context if you're 
the one asking for free help!

> Unfortunately, it' s the only way I can do it, since I want two 
> completely separated phases.

I have no idea what you are referring to by "it". If you make life 
difficult on your reader, you risk them not bothering to read you at 
all. :-)

> With the tools provided by GROMACS I get a mixture, is there a way to 
> get a box with two separated phases?

Sure. With rectangular boxes, it's fairly easy. Decide how much of each 
phase you want, and equilibrate two boxes in NVT whose dimensions are 
chosen to match up. Then use "editconf -translate" to translate one of 
the coordinate files suitably. Then combine the two sets of coordinates 
with a text editor, being sure to keep the format correct and update the 
number of atoms in the case of .gro format. There are some file format 
descriptions on the GROMACS or PDB websites if you need them.


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