[gmx-users] interface

mohammad agha mra_bu at yahoo.com
Tue Feb 21 17:11:34 CET 2012

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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