[gmx-users] octane box help/problems

Chris Shaw chrisbiochem at yahoo.co.uk
Wed Dec 4 22:54:20 CET 2002

Hi All, 

Could someone please help me on this. I am trying to make an octane box by using genconf. I have amended the decane.itp and dec50 files from the distribution, and have arranged a box which I have scaled, using editconf, to the correct density and dimensions 3.0 5.5 4.5 nm. After a run, just octane no waters etc,  the density of the box decreases from 700 to 300. Could anyone tell me where I am going wrong. Otherwise can I put a number of octanes randomly in a water box and let gromacs form a three phase (water octane water) system at the correct density of al three compartments??

I am really stuck and if anyone can please help I would really appreciate it.


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