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
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