On 22/02/2012 10:34 PM, mohammad agha wrote:
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.

What did you expect a liquid in contact with a vacuum to do?


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

First you need to decide how you're going to produce a valid model of *air* which is different from a *vacuum*. Then you need to find parameters for such a model. Then it's the same kind of approach as a mixed-solvent system (see gromacs webpage), only here it will be mixed fluid.

Mark


Best Regards
Sara

------------------------------------------------------------------------
*From:* Mark Abraham <mark.abra...@anu.edu.au>
*To:* Discussion list for GROMACS users <gmx-users@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.

Mark

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