[gmx-users] How to rotate the molecule in box

[sunyeping]

Dear all,

By using the editconf command, we can build a box for the protein molecule, for example:

     gmx editconf -f complex.gro -o newbox.gro -c -d 1.2 -bt cubic  

but how to rotate the molecule in the box? I tried to use "-rotate" option of the editconf command to do so, but I found part of the molecule goes out the pbc box after rotation. Please refer to the image at the following link:

https://drive.google.com/file/d/1P_yTeRSkHpeUTXSUZMlTw2AHZ17s0htv/view?usp=sharing

The molecule was orignally at position 1. I wanted to rotate the molecule around x and y axes by 45 degrees. After I ran the following command:

    gmx editconf -f newbox.gro -rotate 45 45 0 -bt o -o newbpx_1.gro

The molecule went to position 2. You can see part of the molecule are now out of the box. 

Do you know how to rotate the molecule but keep it within the box?

Thank you in advance.

Yeping