[gmx-users] Changing tau_p for parrinello-rahman made my simulation stable
J.Hermann at lrz.tu-muenchen.de
Wed Nov 29 17:27:48 CET 2017
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
More information about the gromacs.org_gmx-users