[gmx-users] gmx traj output

Justin Lemkul jalemkul at vt.edu
Wed Apr 25 03:10:08 CEST 2018

On 4/23/18 11:08 PM, Mohsen Ramezanpour wrote:
> Hi Gromacs users,
> I am using gmx traj to get the box size (X, Y, Z).
> I use the following command:
> echo 0 | gmx traj  -f trajectory.xtc  -s md.tpr  -ob box.xvg  -xvg none
> The output has 77 columns.
> 1st is the time step,
> 2nd, 3rd, and 4th seem to be the X, Y, and Z size of the box.
> I was wondering what are the 5th, 6th, and 7th columns giving, exactly?

The output is the half-matrix of the box tensor. The first three 
elements are the diagonal, the remaining three are the off-diagonal 



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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