[gmx-users] mdrun error

Justin Lemkul jalemkul at vt.edu
Sun Sep 1 19:23:58 CEST 2019

On 9/1/19 7:02 AM, m g wrote:
> Dear Justin,
There are many other people on this list, and I don't always have answers :)

>   I'm simulating a system with "wall" for z direction, but I gave this error in minimization step "software inconsistency error: lost particles while sorting",.Would you please help me? I used the following parameter:

What GROMACS version are you using? CPU or GPU? Does the simulation work 
without the walls? You need to provide a lot more diagnostic 
information. This is a cryptic error that suggests something very 
fundamental is wrong. That also makes it very hard to diagnose.

If you're not using the latest version of GROMACS, start there. I recall 
some bug fixes that may be relevant. If the error is reproducible in 
2019.3, please post a more complete description of what you're doing.


> integrator      =steep
> emtol               = 100.0emstep              = 0.01nsteps                = 5000nstlist               = 1cutoff-scheme       = Verletns_type               = gridrlist               = 1.2    coulombtype         = PMErcoulomb            = 1.2vdwtype             = cutoffvdw-modifier        = force-switchrvdw-switch         = 1.0rvdw                = 1.2            DispCorr            = nopbc                 =xy                    nwall               = 2wall_type           = 10-4wall_r_linpot       = 1wall_atomtype       = ca  cawall_density        = 60  60wall_ewald_zfac     = 3ewald-geometry      = 3dc
> Thanks,Ganj


Justin A. Lemkul, Ph.D.
Assistant Professor
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