[gmx-users] Ions moving to the opposite layer during minimization.

anu chandra anu80125 at gmail.com
Tue Jul 14 12:42:19 CEST 2015

Dear Gromacs users,

I am working with membrane proteins. The system contains CaCl2  ions and I
build the system with calcium ions on one side of the membrane (here, upper
layer) and chloride ions distributed on both side of the membrane, in order
to maintain the physiological condition. Unfortunately, after the very
first minimization, when I visualize the gro file in VMD I have noticed
that  the calcium ions  entered the opposite side of the membrane (ie,
lower layer) and subsequently get distributed in the lower layer during the
equilibration process. Though I have tried with varying Z-dimension values
of the box size, the same has been noticed when visualizing the output gro
file with VMD.

Please help me to figure out what is wrong with my simulation box.

Many thanks

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