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

Hermann, Johannes J.Hermann at lrz.tu-muenchen.de
Wed Nov 29 18:05:11 CET 2017

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 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.
> 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 that.
>> All the best
>> Johannes
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*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

Email: j.hermann at lrz.tum.de

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