[gmx-users] Use NVT to mimic NVE

Dr. Vitaly Chaban vvchaban at gmail.com
Sun Oct 12 17:32:18 CEST 2014

The artifacts are caused by energy leakage. Thermostatting does not
solve them. The problem exists, but you do not see it clearly with
thermostat. For instance, I have an example where a liquid droplet in
vacuum is not stable due to bad energy conservation. Some particles
just sporadically fly away over the course of the simulation.

NVE generally does not like constraints. If I remember correctly from
the previous messages, you use constraints. Novel performance
improvements in gromacs (accumulated after 4.0 and especially after
4.5) sometimes compromise accuracy, though it is a long discussion
itself. What about downgrading to gmx 4.0 or gmx 3.3, after all? The
very last time I used gromacs for NVE simulation was in 2009. I guess
I used gmx 3.3.3 (but maybe 4.0.x). There were no problems for sure.

I would also give a try to some very simple system (e.g. liquid argon)
to observe what happens to total energy.

Good luck with troubleshooting!

Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН

On Sun, Oct 12, 2014 at 4:53 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
>  Firstly, what are the possible errors/artifacts caused by masking "the
> energy leakage problem with the thermostat" in this case?
> Secondly, are there any other mdp setting that I can try to make the mixed
> precision gromacs NVE run have conserved energy over 100 ns ? (and... is it
> because of some errors that I made in my systems that make the NVE run not
> conserved in energy?)
> The NVE has the following statistics.
> Statistics over 2747281 steps [ 0.0000 through 1373.6400 ps ], 4 data sets
> All statistics are over 274729 points
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Disper. corr.              -3961.13          0          0 2.60178e-09
> (kJ/mol)
> Total Energy                -309939        160     337.76    478.828
> (kJ/mol)
> Temperature                 300.292       0.24    1.49289   0.631428  (K)
> Pressure                   -64.5409        4.7    148.779    25.1326  (bar)
> --
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