GROMACS version: 2021.4-Ubuntu-2021.4-2
GROMACS modification: No
nvt.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