[gmx-users] Changing tau_p for parrinello-rahman made my simulation stable
mark.j.abraham at gmail.com
Wed Nov 29 18:15:48 CET 2017
If I faced any issues, then I would use Berendsen NPT until the volume
stabliized, rather than making arbitrary choices of lengths of time for
phases. One is trying to equilibrate, so looking at the longest-timescale
relevant observables makes some sense.
On Wed, Nov 29, 2017 at 6:05 PM Hermann, Johannes <
J.Hermann at lrz.tu-muenchen.de> wrote:
> Hi Mark,
> thank you for your reply. So you would not recommend using tau_p=2.0?
> I did EM, Annealing (1ns), NVT (1ns), NPT (1ns), and then the simulation
> crashes after 15 ns.
> So would you recommend like 10 ns with Berendsen after NPT? Crashing
> after 15ns could still due to not being in equilibrium?
> Thanks in advance!
> All the best
> On 29.11.2017 17:52, Mark Abraham wrote:
> > Hi,
> > 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
> > this might be an idea to avoid. Recent versions of grompp even warn if
> > use that together with generating new velocities. So start with Berendsen
> > and then switch.
> > Mark
> > 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
> >> All the best
> >> Johannes
> >> --
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> *Technische Universität München*
> *Johannes Hermann, M.Sc.*
> Lehrstuhl für Bioverfahrenstechnik
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