[gmx-users] Changing tau_p for parrinello-rahman made my simulation stable

Mark Abraham mark.j.abraham at gmail.com
Wed Nov 29 17:52:36 CET 2017


P-R is well known to be unsuitable for systems that are not yet close to
equilibrium, and documented accordingly.
http://www.gromacs.org/Documentation/Terminology/Blowing_Up also suggests
this might be an idea to avoid. Recent versions of grompp even warn if you
use that together with generating new velocities. So start with Berendsen
and then switch.


On Wed, Nov 29, 2017 at 5:28 PM Hermann, Johannes <
J.Hermann at lrz.tu-muenchen.de> wrote:

> Dear all,
> I had a hard time making my simulation stable. Perhaps someone has an
> explanation, perhaps it (just) saves someone a lot of time. However, I
> want to share my experience:
> I have a dense simulation box (80% water, 20% protein). Free simulation,
> no restrains, constrains on the H-bonds. After some time (around 15ns) I
> always get LINCS warnings, which lead the simulation to stop either
> because of a "Segmentation fault (11)" or "1 particles communicated to
> PME rank 0 are more than 2/3 times the cut-off..". I looked at the
> trajectories but could not identify any strange behavior.
> I tried a lot of things, but what made my simulations eventually stable
> was to increase tau_p for parrinello-rahman from 1.0 to 2.0. Can it be
> guessed whether this value is okay, or will it produce un-physical
> behavior?
> I know I did not provide a lot of specifics about my setup and run
> parameters, I can happily provide that if someone wants to dig deeper that.
> All the best
> Johannes
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