[gmx-users] Duplicate lipid bilayer, simulate protein and remove extra lipid bilayer

Du, Yu duyu at sioc.ac.cn
Thu Oct 12 10:45:04 CEST 2017

Dear GMX Users, 

My question is 512-lipid bilayer is too big. How can I resize it and the cooresponding box size?

I duplicated the 128-lipid bilayer using 
$gmx_mpi genconf -f lipid128.gro -o lipid_new.gro -nbox 2 2 1

But the new 512-lipid bilayer is so large, I want to remove the some lipids according to the x and y coordinate.

I know the parameter -nbox uses integers. But is there any easy way to fulfill the function like `gmx_mpi genconf -f lipid128.gro -o lipid_new.gro -nbox 1.5 1.5 1`?

Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China. 
Zip: 200032, Tel: (86) 021 5492 5275

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