# 1 particles communicated to PME rank 1 are more than 2/3 times the cut-off out of the domain decompo **URL:** \ **Category:** User discussions\ **Tags:** mdp-parameters\ **Created:** [April 9, 2025, 4:59am UTC](https://gromacs.bioexcel.eu/t/1-particles-communicated-to-pme-rank-1-are-more-than-2-3-times-the-cut-off-out-of-the-domain-decompo/11896 "2025-04-09T04:59:03Z")\ **Posts on this page:** 1\ **Page:** 1
**Author:** ![haridhachandran](https://avatars.discourse-cdn.com/v4/letter/h/ce7236/32.png) [@haridhachandran](https://gromacs.bioexcel.eu/u/haridhachandran)\ **Post date:** [April 9, 2025, 4:59am UTC](https://gromacs.bioexcel.eu/t/1-particles-communicated-to-pme-rank-1-are-more-than-2-3-times-the-cut-off-out-of-the-domain-decompo/11896/1 "2025-04-09T04:59:03Z")
GROMACS version: 2021.4-Ubuntu-2021.4-2 GROMACS modification: No [nvt.mdp](https://gromacs.bioexcel.eu/uploads/short-url/2dFZZSzhW6mdHN7GwTlUPWK2Q0T.mdp) (2.6 KB) I have attached my nvt.mdp file, I am getting the same error that is Back Off! I just backed up nvt.log to ./#nvt.log.1# Compiled SIMD: SSE4.1, but for this host/run AVX2\_256 might be better (see log). Reading file nvt.tpr, VERSION 2021.4-Ubuntu-2021.4-2 (single precision) Changing nstlist from 20 to 100, rlist from 1.2 to 1.295 Using 24 MPI threads Using 1 OpenMP thread per tMPI thread Back Off! I just backed up nvt.xtc to ./#nvt.xtc.1# Back Off! I just backed up nvt.edr to ./#nvt.edr.1# starting mdrun ‘Protein in water’ 50000 steps, 50.0 ps. step 1200, will finish Wed Apr 9 10:50:38 2025vol 0.91 imb F 5% pme/F 0.47 Step 1290, time 1.29 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.641675, max 31.958916 (between atoms 24739 and 24706) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 24706 24691 92.8 0.1614 0.1653 0.1614 24723 24691 91.8 0.1421 4.4420 0.1420 24739 24706 91.7 0.0973 3.2053 0.0972 Step 1290, time 1.29 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000119, max 0.010556 (between atoms 24692 and 24708) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 24691 24706 92.8 0.1614 0.1653 0.1614 24706 24739 91.7 0.0973 3.2053 0.0972 24691 24723 91.8 0.1421 4.4420 0.1420 Wrote pdb files with previous and current coordinates Step 1291, time 1.291 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000827, max 0.067385 (between atoms 24692 and 24708) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 24692 24708 45.8 0.1635 0.1727 0.1618 24691 24708 50.9 0.1622 0.1726 0.1618 24691 24701 59.8 0.1625 0.1896 0.1618 24690 24701 58.1 0.1637 0.1887 0.1618 24704 24736 40.0 0.0958 0.1039 0.0972 24691 24706 73.7 0.1653 0.1970 0.1614 24706 24739 93.6 3.2053 0.1478 0.0972 Step 1291, time 1.291 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 1.294687, max 88.813683 (between atoms 24723 and 24691) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 24736 24704 40.0 0.0958 0.1039 0.0972 24692 24708 45.8 0.1635 0.1727 0.1618 24701 24691 59.8 0.1625 0.1896 0.1618 24706 24691 73.7 0.1653 0.1970 0.1614 24708 24691 50.9 0.1622 0.1726 0.1618 24701 24690 58.1 0.1637 0.1887 0.1618 24739 24706 93.6 3.2053 0.1478 0.0972 Wrote pdb files with previous and current coordinates * * * Program: gmx mdrun, version 2021.4-Ubuntu-2021.4-2 Source file: src/gromacs/ewald/pme\_redistribute.cpp (line 305) MPI rank: 11 (out of 24) Fatal error: 1 particles communicated to PME rank 1 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at [Common Errors — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Errors)