[gmx-users] Box dimension in Umbrella Sampling

[SUSHMITA BASU]

Dear users,
I am using Gromacs 2016 to do umbrella sampling of a protein-RNA complex. I am following the Lemkul's tutorial of umbrella sampling, but I couldn't get how the box dimension was determined. I understand why for a pull of 5nm, the z axis of the box is set at 12 nm, but did not get how the x and y axis of the box is determined. This question might be very basic, but I cannot figure out how to do it. Kindly help me in this. Thanks in advance.
Thanks and Regards
Sushmita Basu

Thanks and regards

Sushmita Basu
Research Scholar
Department of Biotechnology
Indian Institute of Technology Kharagpur
Kharagpur 721302, India