# Metadynamics run using GROMACS/2020.4-intel-2020u2-PLUMED-2.7.0 fails **URL:** \ **Category:** User discussions\ **Tags:** mdrun\ **Created:** [April 28, 2021, 4:04am UTC](https://gromacs.bioexcel.eu/t/metadynamics-run-using-gromacs-2020-4-intel-2020u2-plumed-2-7-0-fails/2038 "2021-04-28T04:04:07Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![zmazhar](https://avatars.discourse-cdn.com/v4/letter/z/6bbea6/32.png) [@zmazhar](https://gromacs.bioexcel.eu/u/zmazhar)\ **Post date:** [April 28, 2021, 4:04am UTC](https://gromacs.bioexcel.eu/t/metadynamics-run-using-gromacs-2020-4-intel-2020u2-plumed-2-7-0-fails/2038/1 "2021-04-28T04:04:08Z")
GROMACS version: 2020.4 GROMACS modification: Yes/No (plumed enabled) Here post your question: I am running a Metadynamics simulation with multiple replicas using gromacs (plumed enabled version). It was running fine for two days (22ns) but then I wanted to continue the run beyond 2 days using the checkpoint file. Yet every time it gives me an error along these lines: Program: gmx mdrun, version 2020.4-MODIFIED Source file: src/gromacs/ewald/pme\_redistribute.cpp (line 305) MPI rank: 34 (out of 400) Fatal error: 1711 particles communicated to PME rank 2 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) mdp file: ################# integrator = md dt = 0.002 nsteps = -1 nstxout-compressed = 5000 compressed-x-precision = 1000 nstxout = 50000 nstvout = 50000 nstfout = 0 nstcalcenergy = -1 nstenergy = 5000 nstlog = 10000 ; cutoff-scheme = Verlet nstlist = 20 rlist = 1.2 coulombtype = pme rcoulomb = 1.2 vdwtype = Cut-off vdw-modifier = Force-switch rvdw\_switch = 1.0 rvdw = 1.2 ; pme\_order = 4 ewald\_rtol = 1e-05 ewald-rtol-lj = 0.001 lj-pme-comb-rule = Geometric ewald\_geometry = 3d epsilon\_surface = 0 fourierspacing = 0.12 ; tcoupl = V-rescale nsttcouple = -1 tc\_grps = Protein non-Protein tau\_t = 1.0 1.0 ref\_t = 310 310 ; pcoupl = Parrinello-Rahman pcoupltype = isotropic tau\_p = 1.0 compressibility = 4.5e-5 ref\_p = 1.0 ; constraints = h-bonds constraint\_algorithm = LINCS continuation = no lincs-order = 6 lincs-iter = 2 lincs-warnangle = 30 ; nstcomm = 25 comm\_mode = linear comm\_grps = SYSTEM ; pbc = xyz ; refcoord\_scaling = com gen-seed = -1 ns\_type = grid ############# Job script: ############### #SBATCH -J mnm\_nmr # Name of the job #SBATCH -n 400 #–gres=gpu:1 #SBATCH -N 9 # Number of nodes #SBATCH -t 2-00:00:00 # Runtime in HH:MM:SS #SBATCH --mem-per-cpu=2GB # Memory requested in MB (see also --mem-per-cpu) #SBATCH -o mnm\_nmr\_cont%j.out # File to write STDOUT, %j=jobid #SBATCH -e mnm\_nmr\_cont%j.err # File to wrote STDERR, %j=jobid #SBATCH --mail-type=ALL # Send email when job starts, ends, fails, etc \ # Load the “gromacs” module module load GROMACS/2020.4-intel-2020u2-PLUMED-2.7.0 # Metadynamics Metainference mpirun -np 400 gmx\_mpi mdrun -v -plumed plumed\_mnm\_v5.dat -deffnm mnm -multidir {0..19} -cpi mnm.cpt -maxh 47 -cpt 40 -tunepme yes ############ I have tried troubleshooting using different things but it’s just not working so I decided to reach out for some expert help. I would really appreciate guidance on how to handle this error. P.S. the system looks fine. regards, Zahra ---
**Author:** ![S.Z](https://avatars.discourse-cdn.com/v4/letter/s/da6949/32.png) [@S.Z](https://gromacs.bioexcel.eu/u/S.Z)\ **Post date:** [April 28, 2021, 4:21am UTC](https://gromacs.bioexcel.eu/t/metadynamics-run-using-gromacs-2020-4-intel-2020u2-plumed-2-7-0-fails/2038/2 "2021-04-28T04:21:01Z")
Hi, I believe you have already performed some equilibration steps prior to the current Parrinello-Rahman simulation, however, according the ‘‘continuation = no’’ in your mdp file you are not basically using the equilibrated system. The ‘‘continuation = no’’ means generation of the initial velocity of the particles from scratch. So, try ‘‘continuation = yes’’ and ‘‘gen-vel = no’’ and use (gmx gromp … -t \*.cpt) the checkpoint file of the previous simulation. Regards, Salman ---
**Author:** ![zmazhar](https://avatars.discourse-cdn.com/v4/letter/z/6bbea6/32.png) [@zmazhar](https://gromacs.bioexcel.eu/u/zmazhar)\ **Post date:** [April 28, 2021, 10:59am UTC](https://gromacs.bioexcel.eu/t/metadynamics-run-using-gromacs-2020-4-intel-2020u2-plumed-2-7-0-fails/2038/3 "2021-04-28T10:59:08Z")
Thank you for your recommendation Salman! I will try to follow it and see how it goes. regards, Zahra ---
**Author:** ![zmazhar](https://avatars.discourse-cdn.com/v4/letter/z/6bbea6/32.png) [@zmazhar](https://gromacs.bioexcel.eu/u/zmazhar)\ **Post date:** [April 28, 2021, 4:01pm UTC](https://gromacs.bioexcel.eu/t/metadynamics-run-using-gromacs-2020-4-intel-2020u2-plumed-2-7-0-fails/2038/6 "2021-04-28T16:01:55Z")
Hello, I tried the advised method but it did not help me. I used the following commands: gmx grompp -f metad-metai4\_v2.mdp -p topol.top -t mnm.cpt -c mnm.tpr -o mnm\_v2.tpr And then used this subsequent mdrun command: mpirun -np 400 gmx\_mpi mdrun -v -plumed plumed\_mnm\_v5.dat -deffnm mnm -s mnm\_v2.tpr -multidir {0…19} -cpi mnm.cpt -maxh 47 -cpt 40 -tunepme yes Maybe I am still doing something wrong because the simulation stopped after 3 minutes into the run. Is there anything else I can check. regards, Zahra ---
**Author:** ![zmazhar](https://avatars.discourse-cdn.com/v4/letter/z/6bbea6/32.png) [@zmazhar](https://gromacs.bioexcel.eu/u/zmazhar)\ **Post date:** [April 28, 2021, 4:04pm UTC](https://gromacs.bioexcel.eu/t/metadynamics-run-using-gromacs-2020-4-intel-2020u2-plumed-2-7-0-fails/2038/7 "2021-04-28T16:04:07Z")
HI, I tried the advised method but it did not help me. I used the following commands: gmx grompp -f metad-metai4\_v2.mdp -p topol.top -t mnm.cpt -c mnm.tpr -o mnm\_v2.tpr And then used this subsequent mdrun command: mpirun -np 400 gmx\_mpi mdrun -v -plumed plumed\_mnm\_v5.dat -deffnm mnm -s mnm\_v2.tpr -multidir {0…19} -cpi mnm.cpt -maxh 47 -cpt 40 -tunepme yes Maybe I am still doing something wrong because the simulation stopped after 3 minutes into the run. Is there anything else I can check. ---
**Author:** ![zmazhar](https://avatars.discourse-cdn.com/v4/letter/z/6bbea6/32.png) [@zmazhar](https://gromacs.bioexcel.eu/u/zmazhar)\ **Post date:** [April 28, 2021, 4:06pm UTC](https://gromacs.bioexcel.eu/t/metadynamics-run-using-gromacs-2020-4-intel-2020u2-plumed-2-7-0-fails/2038/8 "2021-04-28T16:06:48Z")
![reply](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/4b93c247ab2f9bff27fc3a4d5d37bfd091b125b1.jpeg) ---
**Author:** ![S.Z](https://avatars.discourse-cdn.com/v4/letter/s/da6949/32.png) [@S.Z](https://gromacs.bioexcel.eu/u/S.Z)\ **Post date:** [April 28, 2021, 11:03pm UTC](https://gromacs.bioexcel.eu/t/metadynamics-run-using-gromacs-2020-4-intel-2020u2-plumed-2-7-0-fails/2038/9 "2021-04-28T23:03:25Z")
Hi Zahra, If it is not an issue with your specific system and the metadynamics simulation which I am not that much into it, then it all gets back to have the system well energy-minimized and well-equilibrated. Some potential solutions could be: 1. Please first try to run the system for one or two ns using a less fancier pressure coupling algorithm likes the Berendsen and then switch to Parrinello. 2. Sometimes changing the maximum considered distance for the bonding interaction would give some more room, so, no hurt of you test something like -rdd 1.2 -dds 0.9999 or around in your gmx mdrun. Cheers, Salman ---
**Author:** ![zmazhar](https://avatars.discourse-cdn.com/v4/letter/z/6bbea6/32.png) [@zmazhar](https://gromacs.bioexcel.eu/u/zmazhar)\ **Post date:** [May 10, 2021, 2:15am UTC](https://gromacs.bioexcel.eu/t/metadynamics-run-using-gromacs-2020-4-intel-2020u2-plumed-2-7-0-fails/2038/10 "2021-05-10T02:15:35Z")
Thank you for your help! Unfortunately, this problem still persists after equilibration so I am thinking that it might be because of a bug of some sorts. regards, Zahra