[gmx-users] velocity-verlet giving nans

[Mark Abraham]

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
problem.

If you want to suggest fixing any possible problem, please file an issue at
redmine.gromacs.org

Cheers,

Mark


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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