[gmx-users] octane box help/problems

[Dallas Warren]

Chris,

>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??

What temperature and coupling are you using? i.e. a copy of md.mdp would be 
handy to see the settings you are using.

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy
Monash University
381 Royal Parade
Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9076
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