[gmx-users] how to reassign velocities in the .mdp file effectively?

[mhuhtala at abo.fi]

> I am trying to test the reproducibility of the md production run.

You can use the options

gen-vel                  = yes
gen-temp                 = 300
gen-seed                 = -1

in your .mdp file and run again. That example will generate new random  
velocities corresponding to 300 K and using a random seed picked  
automatically. Setting "gen-vel = no" will use the existing velocities  
in the starting .gro file. You may need to generate the new velocities  
at an equilibration stage rather than at the beginning of the  
production run, depending on your system.