[gmx-users] interface

mohammad agha mra_bu at yahoo.com
Wed Feb 22 12:34:28 CET 2012

Dear Mark,

Thank you very much from your reply.
I see a box that the half of it consists of water and another half of box is void, but when I run md.mdp for production simulation all of water molecules dispersed in total of box and I don't see interface and total of box filled by water.

Can you help me to construct the air/water interface, Please?

Best Regards

 From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Wednesday, February 22, 2012 12:59 AM
Subject: Re: [gmx-users] interface

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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