[gmx-users] (no subject)
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
> 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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