[gmx-users] unfragmenting molecule in a trajectory

[Irem Altan]

Hi,

I ran a simulation using the output of another simulation. While obtaining this output, I failed to use the -pbc nojump option, so the initial structure for my simulation is a fragmented molecule. This resulted in a trajectory that I can’t unfragment using -pbc nojump. Is there a way to use a file that is the input to the first simulation in order to unfragment the molecule in the second trajectory?

Best,
Irem