[gmx-users] changing the velocity in trajectory file

[Lutz Maibaum]

On Nov 29, 2010, at 8:52 PM, sreelakshmi ramesh wrote:
> Lutz ya you are true but as you said how can i change the velocity  for a config every move as in TPS?since i have not done tps i have no idea abt this.

You can't, neither for TPS nor for FFS. I don't think Gromacs provides this functionality. You will have to write your own code that reads positions and velocities from a trajectory file, modifies the velocities, and writes positions and velocities to a file that Gromacs can use as an initial configuration.

Alternatively, you can use a stochastic integrator (like Brownian dynamics) and set ld_seed to -1. This way, even identical initial configurations will result in different trajectories.

  -- Lutz