Basic doubt regarding editconf

User discussions
1

GROMACS version: 5.1.4
GROMACS modification: No

Respected community members,

I have a very basic doubt that I would like to ask. Sorry for my ignorance. I am working on protein ligand simulation following the tutorials by Dr. Lemkul. I have enclosed my protein in a cubic box by using the following command:

Command line:

gmx editconf -f ComplexWT.gro -o complex_box.gro -bt cubic -c -d 1.5

I got the following output:

Read 7520 atoms

Volume: 0 nm^3, corresponds to roughly 0 electrons

No velocities found

system size : 6.055 7.241 5.252 (nm)

diameter : 7.488 (nm)

center : 8.346 5.001 4.642 (nm)

box vectors : 0.000 0.000 0.000 (nm)

box angles : 0.00 0.00 0.00 (degrees)

box volume : 0.00 (nm^3)

shift : -3.101 0.243 0.602 (nm)

new center : 5.244 5.244 5.244 (nm)

new box vectors : 10.488 10.488 10.488 (nm)

new box angles : 90.00 90.00 90.00 (degrees)

new box volume :1153.79 (nm^3)

My basic doubt is why box vectors, angles, and volume are written twice. Also, why initial box vectors, angles and volume are shown as 0. Am I doing some thing worng?

2

Respected community members,

I guess my question went unnoticed. I am really hoping for someone to help me with this.

Thanks in advance

3

In terms of what it prints out, it depends on what you provide to the program in the input coordinate file. It prints twice to give you (as it says) the initial and new values of the box attributes.