[gmx-users] Initial velocities before equilibration

[John Whittaker]

Hi,

> After completing MD production run, I ran a command gmx check for my xtc
> file. However, no velocities were updated in any frame.

http://manual.gromacs.org/documentation/2016/user-guide/file-formats.html

The .xtc trajectory filetype does not support velocities or forces, only
positions.

In order to store the velocities throughout a run, your simulation must
output a .trr file. Have a look at the mdp options:

http://manual.gromacs.org/documentation/5.1/user-guide/mdp-options.html

under the section "output control".

John