[gmx-users] Exploding temp/pressure.

[Daniel Bauer]

Did you forget to set an initial temperature distribution? In your mdp you
set gen_vel to no. So it will not create an initial velocity distribution
matching your temperature. For the first simulation of your workflow, you
should set gen_vel: yes and continuation: no. Then for all simulation that
build on top of that simulation you use the velocities from the last
timestep of the previous one (mdrun -t flag) and disable gen_vel + set
continuation to yes.

Also consider running your first simulation with berenden barostat to
quickly equilibrate the pressure. For actual sampling of the configuration
space you should then switch to parrinello since berendson doesnt sample
the ensemble correctly.

Both temperature and pressure should equilibrate very quickly in a martini
simulation, allowing to increase the timestep to 3 fs or more rather
quickly.


Hope this helps!
Daniel