GROMACS version: 2018.8
I used .xtc file format to store the trajectories of my previous simulations. But now I need the forces and velocities to do some analysis. The simple way is to start the simulation from the very beginning with a new .mdp file, but it is also very time-consuming. I am wondering can I use the existing .xtc and the mdrun -rerun function to get the .trr file. Are the forces and velocities as accurate as the result got by completely running the simulation again?
Any help would be much appreciated!
The forces will be accurate. Velocities from reruns are not trustworthy, and I’m not sure if they are even calculated.
Thank you very much!
Then I need to start the simulation from the beginning but set the output format to .trr.
You also need to specify a non-zero value of nstvout in the .mdp file; output options related to bulky .trr files are disabled by default, even if you tell mdrun to write one, it will only contain the data you request.
Hello,
Thank you very much for reminding me!
I have found that it has separate options for different properties by nstxout, nstvout and nstfout.