[gmx-users] interface

mohammad agha mra_bu at yahoo.com
Wed Feb 22 12:31:22 CET 2012

Dear Dr. Warren,

Thank you very much from your response. 

When I see the coordinate file, there is a box consists of water in half of it and another half of box is void, but when I do md.mdp for production simulation, all of water molecules are dispersed in total of box.

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

Best Regards

 From: Dallas Warren <Dallas.Warren at monash.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Wednesday, February 22, 2012 4:26 AM
Subject: RE: [gmx-users] interface

What does it look like when you visualise the coordinate file?  That is how you can answer that question, as we certainly can’t.
And as you will soon find out, you cannot have a single interface in a simulation box, you have to have two.
Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
When the only tool you own is a hammer, every problem begins to resemble a nail.
From:gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of mohammad agha
Sent: Wednesday, 22 February 2012 3:12 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] interface
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?
Please help me.
Best Regards
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