[gmx-users] Reg: Putting molecules on one side of the box

Mark Abraham mark.abraham at anu.edu.au
Fri Sep 24 09:28:59 CEST 2010

Use genconf to replicate some suitable smaller box of decane to the full size, delete the second half of the decane molecules, then use genbox to fill the rest with water. Cunning use of genconf should allow you to select where the division lies.


----- Original Message -----
From: vinothkumar mohanakrishnan <kmvinoth at gmail.com>
Date: Friday, September 24, 2010 17:22
Subject: [gmx-users] Reg: Putting molecules on one side of the box
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> Hi all
> I have a triclinic box of length of 8*3*3 nm. i want to put water on one side of the box and say decane on the other side of the box. How to generate .gro for the water-decane mixture such that they form two distinct parts of the box.
> Regards
> Vinoth
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