[gmx-users] interface

Mark Abraham Mark.Abraham at anu.edu.au
Tue Feb 21 22:29:16 CET 2012

On 22/02/2012 3:11 AM, mohammad agha wrote:
> Dear Gromacs Specialists,
> I made a box consists of water with box lengths:  6nm  * 6nm  * 6nm , 
> then I equilibrated it with NPT ensemble, box size increased to 
> 6.66176, then I kept the /x-/ and /y-/dimensions fixed, and double the 
> system size in /z as following:/
> /editconf -f pr1.gro -o newbox1.gro -box 6.66176 6.66176 13.32352 
> -center 3.33088 3.33088 3.33088
> Next that, I placed one surfactant in center of water phase as following:/
> /editconf -f surfactant.gro -o newbox-cta.gro -box 6.66176 6.66176 
> 13.32352 -center 3.33088 3.33088 1.66544
> genbox -cp newbox-cta.gro -cs newbox1.gro -o newbox2.gro/
> /and I added one ion to my system, then ran md.mdp for production 
> simulation.
> /
> /Do I have one air/water interface in my system?/

You need to use visualization software and see if the configuration 
looks like you intend it to look. You certainly don't have an air-water 
interface if one of them is vacuum.

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