[gmx-users] how to put protein in the box?

Seonah Kim kim at qtp.ufl.edu
Sun Jun 27 02:31:03 CEST 2004

Dear All,

I am using Trpcage with water model.
When I run VMD, I want to put protein in the octahedron box. But my protein is 
jumping a lot sometimes it is in the box but sometimes is out of the box.

I tried to use -center option when I use trjconv, like trjconv -f aaa.trr -o 
aaa.xtc -center, it doesn't work.

Would you tell me the right way to solve this problem?

Thank you.

Seonah Kim

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