[gmx-users] How to generate multiple diverse trajectories from one checkpoint file

[Bin Zhang]

Hi, everyone:

I am testing some transition path sampling (TPS) algorithms using GROMACS.
For certain type of TPS methods, such as the weighted ensemble method, it
requires to restart multiple simulations from a checkpoint and those
simulations needs to be stochastic. In other words, the trajectories
generated from the same checkpoint must be different from each other.

I am wondering what is the best way to do this.

Suppose the overdamped Brownian dynamics (bd) thermostat is used, I think
one can just start (not restart) multiple simulations with different random
seeds from the structure of the checkpoint because the previous velocities
do not matter.

If the Langevin thermostat (sd) is used, is it possible to specify the
random seed when restarting a simulation?

Your advice or suggestions will be much appreciated and welcomed. Thank
you.


Bin W. Zhang