# Restart a 1GPU simulation with 2GPU fails **URL:** \ **Category:** User discussions\ **Created:** [May 27, 2020, 4:49pm UTC](https://gromacs.bioexcel.eu/t/restart-a-1gpu-simulation-with-2gpu-fails/200 "2020-05-27T16:49:35Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![sperezconesa](https://avatars.discourse-cdn.com/v4/letter/s/4af34b/32.png) [@sperezconesa](https://gromacs.bioexcel.eu/u/sperezconesa)\ **Post date:** [May 27, 2020, 4:49pm UTC](https://gromacs.bioexcel.eu/t/restart-a-1gpu-simulation-with-2gpu-fails/200/1 "2020-05-27T16:49:35Z")
GROMACS version: 2020.1 GROMACS modification: No Dear gmx community, I have restarted a simulation with 2 GPUs that was running with 1 GPU before. I get dd\_dump\_error\*pdb and errors and the job fails. Is this normal? The log has this output: ```nohighlight Program: gmx mdrun, version 2020.1 Source file: src/gromacs/domdec/domdec_topology.cpp (line 421) MPI rank: 0 (out of 8) Fatal error: 3700 of the 238965 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.21815 nm) or the two-body cut-off distance (1.59775 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ``` Thanks a lot! Sergio ---
**Author:** ![mijiddorj](https://avatars.discourse-cdn.com/v4/letter/m/779978/32.png) [@mijiddorj](https://gromacs.bioexcel.eu/u/mijiddorj)\ **Post date:** [May 28, 2020, 6:53am UTC](https://gromacs.bioexcel.eu/t/restart-a-1gpu-simulation-with-2gpu-fails/200/2 "2020-05-28T06:53:49Z")
Hi, can you tell me nstlist values in your mdp file. ---
**Author:** ![sperezconesa](https://avatars.discourse-cdn.com/v4/letter/s/4af34b/32.png) [@sperezconesa](https://gromacs.bioexcel.eu/u/sperezconesa)\ **Post date:** [May 29, 2020, 7:31am UTC](https://gromacs.bioexcel.eu/t/restart-a-1gpu-simulation-with-2gpu-fails/200/3 "2020-05-29T07:31:50Z")
Here you go: nstlist=10 I’ll put the rest of mdp for reference ```nohighlight integrator = md ; md tinit = 0 dt = 0.002 nsteps = 25000000 init_step = 0 comm-mode = Linear nstcomm = 100 comm-grps = all nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 10000 nstcalcenergy = -1 nstenergy = 1000 nstxout-compressed = 10000 compressed-x-precision = 1000 energygrps = cutoff-scheme=Verlet nstlist = 10 ns_type = grid pbc = xyz periodic_molecules = no coulombtype = PME rcoulomb = 1.2 vdw-type = Cut-off rvdw-switch = 1.0 rvdw = 1.2 vdw-modifier = Force-switch DispCorr = no fourierspacing = 0.15 pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 tcoupl = Berendsen tc-grps = protein waters_or_ions resname_POPC_POPS_CHL1 tau-t = 0.5 0.5 0.5 ref-t = 310 310 310 pcoupl = Berendsen pcoupltype = semiisotropic nstpcouple = -1 tau-p = 5.0 compressibility = 4.5e-5 4.5e-5 ref-p = 1.0 1.0 refcoord_scaling = No gen_vel = yes gen-temp = 310 gen-seed = -1 constraints = h-bonds constraint-algorithm = Lincs continuation = no lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 ``` Thank you! ---
**Author:** ![mijiddorj](https://avatars.discourse-cdn.com/v4/letter/m/779978/32.png) [@mijiddorj](https://gromacs.bioexcel.eu/u/mijiddorj)\ **Post date:** [May 29, 2020, 3:57pm UTC](https://gromacs.bioexcel.eu/t/restart-a-1gpu-simulation-with-2gpu-fails/200/4 "2020-05-29T15:57:57Z")
I would like to suggest you to use smaller nstlist or gen\_vel = no. ---
**Author:** ![sperezconesa](https://avatars.discourse-cdn.com/v4/letter/s/4af34b/32.png) [@sperezconesa](https://gromacs.bioexcel.eu/u/sperezconesa)\ **Post date:** [June 1, 2020, 7:43am UTC](https://gromacs.bioexcel.eu/t/restart-a-1gpu-simulation-with-2gpu-fails/200/5 "2020-06-01T07:43:54Z")
I am affraid this didn’t work. Not even with nstlist=1. ---
**Author:** ![pszilard](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/pszilard/32/21_2.png) [@pszilard](https://gromacs.bioexcel.eu/u/pszilard)\ **Post date:** [June 1, 2020, 12:23pm UTC](https://gromacs.bioexcel.eu/t/restart-a-1gpu-simulation-with-2gpu-fails/200/6 "2020-06-01T12:23:58Z")
If tolerance-based list buffer estimate is used (default, see `verlet-buffer-tolerance`), `nstlist` is a free parameter and can be set arbitrarily an `mdrun` itself tunes it at startup. Hence, changing `nstlist` in the mdp might not even have an effect on the actual value used at runtime. ---
**Author:** ![sperezconesa](https://avatars.discourse-cdn.com/v4/letter/s/4af34b/32.png) [@sperezconesa](https://gromacs.bioexcel.eu/u/sperezconesa)\ **Post date:** [June 3, 2020, 9:09am UTC](https://gromacs.bioexcel.eu/t/restart-a-1gpu-simulation-with-2gpu-fails/200/7 "2020-06-03T09:09:03Z")
Any other ideas to fix this? ---
**Author:** ![mijiddorj](https://avatars.discourse-cdn.com/v4/letter/m/779978/32.png) [@mijiddorj](https://gromacs.bioexcel.eu/u/mijiddorj)\ **Post date:** [June 5, 2020, 5:50am UTC](https://gromacs.bioexcel.eu/t/restart-a-1gpu-simulation-with-2gpu-fails/200/8 "2020-06-05T05:50:28Z")
How long did you equilibrated your system? Did you try to remove the gen\_vel in this run? I suggest you to additional short equilibration under NVT condition using gen\_vel before this run. Then you can run npt production without gen\_vel, even in multiple replicas. ---
**Author:** ![sperezconesa](https://avatars.discourse-cdn.com/v4/letter/s/4af34b/32.png) [@sperezconesa](https://gromacs.bioexcel.eu/u/sperezconesa)\ **Post date:** [June 5, 2020, 6:03am UTC](https://gromacs.bioexcel.eu/t/restart-a-1gpu-simulation-with-2gpu-fails/200/9 "2020-06-05T06:03:01Z")
The system is well equilibrated (ns) and stable if I don’t change the number of GPUs. The problem must be in a more algorithmical problem. ---
**Author:** ![mijiddorj](https://avatars.discourse-cdn.com/v4/letter/m/779978/32.png) [@mijiddorj](https://gromacs.bioexcel.eu/u/mijiddorj)\ **Post date:** [June 5, 2020, 8:38am UTC](https://gromacs.bioexcel.eu/t/restart-a-1gpu-simulation-with-2gpu-fails/200/10 "2020-06-05T08:38:26Z")
Please check in different versions.