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.war...@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-boun...@gromacs.org [mailto:gmx-users-boun...@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 Sara
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