[gmx-users] Lincs Errors Crashing Simulation

Mark Abraham mark.j.abraham at gmail.com
Sat Apr 21 14:26:05 CEST 2018


The Berendsen weak coupling algorithms are more tolerant of starting
configurations that need significant relaxation. Start with them, then
equilibrate further if you want to use the better ensembles available.


On Sat, Apr 21, 2018, 09:02 Eric Smoll <ericsmoll at gmail.com> wrote:

> Hello,
> I am using gromacs 2018.1.
> Although several steps of an all-atom simulation proceed without problem
> (minimization, NVT and NPT runs with berendsen temperature and pressure
> control), attempts to equilibrate the system with the md integrator under
> NVT conditions with a nose-hoover thermostat and a 1 fs time-step generates
> lincs errors because of extreme molecular distortion.
> Viewing a molecule that distorts and crashes the simulation seems to
> suggest that this molecule has normal dynamics for thousands of timesteps.
> Then, for a few ps before the crash, the molecule starts to show increasing
> amounts of distortion before snapping to an extremely distorted state.
> Any suggestions on how I can troubleshoot this problem?
> Best,
> Eric
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