[gmx-users] Periodicity in x-y plane

Neda Rafiee nerafiee at ipm.ir
Mon Feb 6 08:43:56 CET 2017

Hi. I have already built a lipid bilayer and I want to create a box for it and fill it with water. I used : 
$ gmx editconf -f renumber.gro -o newbox.gro  -c -box 8 8 14 -bt triclinic  
and after that I used:
$ gmx solvate -cp newbox.gro -cs tip4p.gro -o solvated.gro -p topol.top  

but when I see solvated.gro in VMD, in periodicity , I check x +x or y +y direction, I see man water molecules between adjacent neighbors in x-y direction and it destroy the periodicity of my membrane in x-y plane, while I want to have water only in the upper and lower sides of the membrane. What should I do? 

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