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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