[gmx-users] velocity-verlet giving nans

[Sikandar Mashayak]

Hi

I first performed a simulation using leap-frog integrator, which went well
and got the expected results. For post-processing I want velocities at full
time step, but, as per my understanding, leap-frog computes and writes
velocities at half-time step. Therefore, I just changed integrator from
'md' to 'md-vv', i.e., velocity verlet. Unfortunately, after this change in
.mdp file (i.e. keeping all other settings exactly same as previous
leap-frog run) when I run 'mdrun' I am getting 'nan' in output from the
first step itself.

So I am wondering what could be the reason for this behavior of 'md-vv'
integrator.

Thanks
Sikandar