[gmx-users] velocity-verlet giving nans

Mark Abraham mark.j.abraham at gmail.com
Fri Jun 7 16:52:22 CEST 2013

Don't know, but re-interpreting the old velocities at a new time might not
be fully integrated with things calculated from the old velocities, such as
temperature-coupling quantities. For switching integrators, you will need
to re-equilibrate, so you may as well generate new velocities and avoid the

If you want to suggest fixing any possible problem, please file an issue at



On Thu, Jun 6, 2013 at 4:38 AM, Sikandar Mashayak <symashayak at gmail.com>wrote:

> 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
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