# Gmx mdrun is stuck at step=0 **URL:** \ **Category:** User discussions\ **Tags:** mdrun, simulation-setup\ **Created:** [September 13, 2023, 8:37pm UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-is-stuck-at-step-0/7185 "2023-09-13T20:37:40Z")\ **Posts on this page:** 20\ **Page:** 1
**Author:** ![Ali\_Jafari](https://avatars.discourse-cdn.com/v4/letter/a/ee59a6/32.png) [@Ali\_Jafari](https://gromacs.bioexcel.eu/u/Ali_Jafari)\ **Post date:** [September 13, 2023, 8:37pm UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-is-stuck-at-step-0/7185/1 "2023-09-13T20:37:40Z")
GROMACS version: 2020.7 GROMACS modification: No Here post your question Hello everyone I’ve attempted to make a solvent box for acetonitrile in 45C; in charmm36 forcefield but my NVT calculation seams stuck at step=0 I have 6000 atoms in my system and I successfully performed a 50000 step energy minimization. \*Bellow is the .mdp file that I used integrator = md nsteps = 100000 dt = 0.002 nstxout = 500 nstvout = 500 nstenergy = 500 nstlog = 500 rlist = 1.0 coulombtype = cut-off cutoff-scheme = verlet rcoulomb = 1.3 rvdw = 1.3 tcoupl = V-rescale tc-grps = system tau\_t = 0.1 ref\_t = ? pcoupl = no pbc =xyz gen-vel = yes gen-temp = ? I’ve already tried ?=298 and 318 but no luck so far I appreciate any help in advance. ---
**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Post date:** [September 14, 2023, 5:06am UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-is-stuck-at-step-0/7185/2 "2023-09-14T05:06:08Z")
Could you copy-paste all the messages you got in either the terminal or output file (so any notes, warnings, errors, etc.) when you tried running NVT? ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [September 14, 2023, 6:38am UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-is-stuck-at-step-0/7185/3 "2023-09-14T06:38:48Z")
50000 steps of energy minimization sound like a lot. Maybe your initial configuration has some issues. What is the largest force at the end of the energy minimization? ---
**Author:** ![Ali\_Jafari](https://avatars.discourse-cdn.com/v4/letter/a/ee59a6/32.png) [@Ali\_Jafari](https://gromacs.bioexcel.eu/u/Ali_Jafari)\ **Post date:** [September 14, 2023, 7:07am UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-is-stuck-at-step-0/7185/4 "2023-09-14T07:07:14Z")
this is from the .log file for Energy minimization Step Time 2773 2773.00000 Energies (kJ/mol) Angle Proper Dih. LJ-14 Coulomb-14 LJ (SR) 1.74628e+03 8.40844e+00 -8.17765e+02 -5.48984e+04 -8.61113e+03 Coulomb (SR) Potential Pressure (bar) Constr. rmsd -5.33882e+03 -6.79114e+04 1.07928e+04 9.88824e-07 ``` Step Time 2774 2774.00000 Step Time 2775 2775.00000 Step Time 2776 2776.00000 ``` Energy minimization has stopped, but the forces have not converged to the requested precision Fmax \< 10 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) Steepest Descents converged to machine precision in 2777 steps, but did not reach the requested Fmax \< 10. Potential Energy = -6.7911422e+04 Maximum force = 7.9560303e+03 on atom 1793 Norm of force = 1.8530257e+02 ---
**Author:** ![Ali\_Jafari](https://avatars.discourse-cdn.com/v4/letter/a/ee59a6/32.png) [@Ali\_Jafari](https://gromacs.bioexcel.eu/u/Ali_Jafari)\ **Post date:** [September 14, 2023, 7:10am UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-is-stuck-at-step-0/7185/5 "2023-09-14T07:10:54Z")
Unfortunately I closed the terminal window but here is the last part of my .log file for NVT calculation: Input Parameters: integrator = md tinit = 0 dt = 0.002 nsteps = 100000 init-step = 0 simulation-part = 1 comm-mode = Linear nstcomm = 100 bd-fric = 0 ld-seed = 267344549 emtol = 10 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstcalcenergy = 100 nstenergy = 500 nstxout-compressed = 0 compressed-x-precision = 1000 cutoff-scheme = Verlet nstlist = 10 pbc = xyz periodic-molecules = false verlet-buffer-tolerance = 0.005 rlist = 1.378 coulombtype = Cut-off coulomb-modifier = Potential-shift rcoulomb-switch = 0 rcoulomb = 1.3 epsilon-r = 1 epsilon-rf = inf vdw-type = Cut-off vdw-modifier = Potential-shift rvdw-switch = 0 rvdw = 1.3 DispCorr = No table-extension = 1 fourierspacing = 0.12 fourier-nx = 0 fourier-ny = 0 fourier-nz = 0 pme-order = 4 ewald-rtol = 1e-05 ewald-rtol-lj = 0.001 lj-pme-comb-rule = Geometric ewald-geometry = 0 epsilon-surface = 0 tcoupl = V-rescale nsttcouple = 10 nh-chain-length = 0 print-nose-hoover-chain-variables = false pcoupl = No pcoupltype = Isotropic nstpcouple = -1 tau-p = 1 compressibility (3x3): compressibility[0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compressibility[1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compressibility[2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p (3x3): ref-p[0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p[1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p[2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} refcoord-scaling = No posres-com (3): posres-com[0]= 0.00000e+00 posres-com[1]= 0.00000e+00 posres-com[2]= 0.00000e+00 posres-comB (3): posres-comB[0]= 0.00000e+00 posres-comB[1]= 0.00000e+00 posres-comB[2]= 0.00000e+00 QMMM = false QMconstraints = 0 QMMMscheme = 0 MMChargeScaleFactor = 1 qm-opts: ngQM = 0 constraint-algorithm = Lincs continuation = false Shake-SOR = false shake-tol = 0.0001 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 nwall = 0 wall-type = 9-3 wall-r-linpot = -1 wall-atomtype[0] = -1 wall-atomtype[1] = -1 wall-density[0] = 0 wall-density[1] = 0 wall-ewald-zfac = 3 pull = false awh = false rotation = false interactiveMD = false disre = No disre-weighting = Conservative disre-mixed = false dr-fc = 1000 dr-tau = 0 nstdisreout = 100 orire-fc = 0 orire-tau = 0 nstorireout = 100 free-energy = no cos-acceleration = 0 deform (3x3): deform[0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} simulated-tempering = false swapcoords = no userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 applied-forces: electric-field: x: E0 = 0 omega = 0 t0 = 0 sigma = 0 y: E0 = 0 omega = 0 t0 = 0 sigma = 0 z: E0 = 0 omega = 0 t0 = 0 sigma = 0 density-guided-simulation: active = false group = protein similarity-measure = inner-product atom-spreading-weight = unity force-constant = 1e+09 gaussian-transform-spreading-width = 0.2 gaussian-transform-spreading-range-in-multiples-of-width = 4 reference-density-filename = reference.mrc nst = 1 normalize-densities = true adaptive-force-scaling = false adaptive-force-scaling-time-constant = 4 grpopts: nrdf: 17997 ref-t: 300 tau-t: 0.1 annealing: No annealing-npoints: 0 acc: 0 0 0 nfreeze: N N N energygrp-flags[0]: 0 Changing nstlist from 10 to 25, rlist from 1.378 to 1.548 Using 1 MPI thread Non-default thread affinity set, disabling internal thread affinity Using 8 OpenMP threads System total charge: 0.000 Potential shift: LJ r^-12: -4.292e-02 r^-6: -2.072e-01, Coulomb -8e-01 Generated table with 1273 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1273 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1273 data points for 1-4 LJ12. Tabscale = 500 points/nm Using SIMD 4x8 nonbonded short-range kernels Using a dual 4x8 pair-list setup updated with dynamic pruning: outer list: updated every 25 steps, buffer 0.248 nm, rlist 1.548 nm inner list: updated every 4 steps, buffer 0.021 nm, rlist 1.321 nm At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be: outer list: updated every 25 steps, buffer 0.322 nm, rlist 1.622 nm inner list: updated every 4 steps, buffer 0.030 nm, rlist 1.330 nm Using Lorentz-Berthelot Lennard-Jones combination rule Removing pbc first time ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ G. Bussi, D. Donadio and M. Parrinello Canonical sampling through velocity rescaling J. Chem. Phys. 126 (2007) pp. 014101 -------- -------- — Thank You — -------- -------- There are: 6000 Atoms Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest Initial temperature: 297.989 K Started mdrun on rank 0 Wed Sep 13 23:49:04 2023 ``` Step Time 0 0.00000 ``` Energies (kJ/mol) Bond Angle Proper Dih. LJ-14 Coulomb-14 1.65121e+02 1.78406e+03 1.01411e+03 -8.17716e+02 -5.48976e+04 LJ (SR) Coulomb (SR) Potential Kinetic En. Total Energy -9.65450e+03 -3.29584e+03 -6.57024e+04 4.52880e+04 -2.04144e+04 Conserved En. Temperature Pressure (bar) -2.04144e+04 6.05311e+02 7.87726e+03 ---
**Author:** ![Ali\_Jafari](https://avatars.discourse-cdn.com/v4/letter/a/ee59a6/32.png) [@Ali\_Jafari](https://gromacs.bioexcel.eu/u/Ali_Jafari)\ **Post date:** [September 14, 2023, 7:13am UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-is-stuck-at-step-0/7185/6 "2023-09-14T07:13:31Z")
I can upload my .gro and .top files for solvent box if it can help ---
**Author:** ![MichelePellegrino](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/michelepellegrino/32/628_2.png) [@MichelePellegrino](https://gromacs.bioexcel.eu/u/MichelePellegrino)\ **Post date:** [September 14, 2023, 9:20am UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-is-stuck-at-step-0/7185/7 "2023-09-14T09:20:48Z")
Could this be a case of [PBC wrapping hangs after a system explodes (#4766) · Issues · GROMACS / GROMACS · GitLab](https://gitlab.com/gromacs/gromacs/-/issues/4766)? ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [September 14, 2023, 11:19am UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-is-stuck-at-step-0/7185/8 "2023-09-14T11:19:14Z")
Maybe. But in that case it wouldn’t hang at step 0, but at step nstlist. To check that run: mdrun -v -stepout 1 and see at which step it hangs. The cause of this is likely too high forces. The largest force after EM is far too large. Likely there is some problem in the initial structure. Do a visual inspection of atom 1793 and its surroundings. ---
**Author:** ![Ali\_Jafari](https://avatars.discourse-cdn.com/v4/letter/a/ee59a6/32.png) [@Ali\_Jafari](https://gromacs.bioexcel.eu/u/Ali_Jafari)\ **Post date:** [September 14, 2023, 8:12pm UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-is-stuck-at-step-0/7185/9 "2023-09-14T20:12:58Z")
By using -stepout 1 option, calculation hangs at step 24 gmx mdrun -v -deffnm Acetonitrile\_NVT -ntomp 8 -ntmpi 1 -stepout 1 Back Off! I just backed up Acetonitrile\_NVT.log to ./#Acetonitrile\_NVT.log.1# Reading file Acetonitrile\_NVT.tpr, VERSION 2020.7 (single precision) Changing nstlist from 10 to 25, rlist from 1.378 to 1.548 Using 1 MPI thread Non-default thread affinity set, disabling internal thread affinity Using 8 OpenMP threads Back Off! I just backed up Acetonitrile\_NVT.trr to ./#Acetonitrile\_NVT.trr.1# Back Off! I just backed up Acetonitrile\_NVT.edr to ./#Acetonitrile\_NVT.edr.1# starting mdrun ‘ICE’ 100000 steps, 200.0 ps. step 24 ---
**Author:** ![Ali\_Jafari](https://avatars.discourse-cdn.com/v4/letter/a/ee59a6/32.png) [@Ali\_Jafari](https://gromacs.bioexcel.eu/u/Ali_Jafari)\ **Post date:** [September 14, 2023, 8:20pm UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-is-stuck-at-step-0/7185/10 "2023-09-14T20:20:25Z")
this is the .mdp file that I used for EM integrator = steep nsteps = ? rlist = 1.0 coulombtype = cut-off cutoff-scheme = verlet rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 pbc = xyz periodic\_molecules = yes constraints = all-bonds \*\* I don’t know why but my EM always stops at a number too smaller that nsteps = ? (I even added emtol = 10 and nsteps = 500000 but still EM stopped at 2777) ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [September 15, 2023, 8:26am UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-is-stuck-at-step-0/7185/11 "2023-09-15T08:26:51Z")
I assume mdrun sets nstlist to 25, so indeed mdrun is likely is an extremely long loop to fix PBC because an atom experienced an extremely high force. There seems to be an issue in your initial coordinates which prevents energy minimization from reaching a reasonable state. I can’t say what that issue is. As said, have a look at the environment of atoms 1793 which reports the largest force. ---
**Author:** ![Ali\_Jafari](https://avatars.discourse-cdn.com/v4/letter/a/ee59a6/32.png) [@Ali\_Jafari](https://gromacs.bioexcel.eu/u/Ali_Jafari)\ **Post date:** [September 17, 2023, 8:28pm UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-is-stuck-at-step-0/7185/12 "2023-09-17T20:28:09Z")
I actually checked it and found nothing strange. I must add that every time I’m running EM the atom experiencing highest force changes Would you please explian briefly what should I do(I mean the process of making a solvent box for acetonitrile in charmm36 force field)? Maybe I’m missing something here ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [September 18, 2023, 8:12am UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-is-stuck-at-step-0/7185/13 "2023-09-18T08:12:55Z")
I don’t know how you have prepared your system and the issue can be very case specific. A general thing you can try is running energy minimization with a double precision binary. That will likely get you to a smaller force, but this might not solve your issue. ---
**Author:** ![Sashen123](https://avatars.discourse-cdn.com/v4/letter/s/eb8c5e/32.png) [@Sashen123](https://gromacs.bioexcel.eu/u/Sashen123)\ **Post date:** [September 3, 2024, 9:31pm UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-is-stuck-at-step-0/7185/14 "2024-09-03T21:31:06Z")
Hi All, I am getting an error at 0 step in energy minimization. There is nothing strange when i check the visualization of my input structure (80 molecules - this is a supercell). I didnt get any errors when minimizing a single molecule or 2 molecules (unitcell). Tolerance (Fmax) = 2.00000e+00 Number of steps = 50000 Step= 0, Dmax= 1.0e-02 nm, Epot= 4.68220e+35 Fmax= inf, atom= 101 [cascade040:33746] \*\*\* Process received signal \*\*\* [cascade040:33746] Signal: Segmentation fault (11) [cascade040:33746] Signal code: Address not mapped (1) [cascade040:33746] Failing at address: 0x7f6693bf76f0 Segmentation fault ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [September 4, 2024, 5:31am UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-is-stuck-at-step-0/7185/15 "2024-09-04T05:31:06Z")
Hi, We are trying to avoid segmentation faults as far as possible, so there is certainly room for improvement here. Which version are you using? But the problem here is that the potential energy is huge. I would suspect that the problem is related to the periodic box. - How did you generate that “supercell”? - What are the dimensions of the periodic box? - You say that there is nothing strange when you visualize the 80 molecules, but you don’t say what you checked. - Does it look correct when you show the periodic box? - Does it look correct when you show the periodic images in all directions (from the Graphical Representations window in VMD)? - What molecule is this? - Are there any periodic bonds, i.e. bonds across the periodic boundary? ---
**Author:** ![Sashen123](https://avatars.discourse-cdn.com/v4/letter/s/eb8c5e/32.png) [@Sashen123](https://gromacs.bioexcel.eu/u/Sashen123)\ **Post date:** [September 4, 2024, 6:58am UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-is-stuck-at-step-0/7185/16 "2024-09-04T06:58:05Z")
Hi Magnus, Thank you very much for your reply. My Gromacs version is 2019.6. Supercell was generated using the unit cell and packing from genconf command. I have tried several dimensions Try 1 - 3.78250 3.08088 3.29836 (this with using the exact angles of the unit cell. Try 2 - 3.78250 3.08088 3.29836 using these dimensions but centering the supercell using editconf. Try 3 and 4 - 10 10 10 and 15 15 15 cubic boxes (to avoid PBC interactions) # got the same error in all trials It looks correct in periodic box as well as the periodic images. The molecule is Tips pentacene No any periodic bonds. ![Screenshot 2024-09-04 025717](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/0/0234482966a2bfe3242681b9873829fb9bc38805.jpeg) ---
**Author:** ![Sashen123](https://avatars.discourse-cdn.com/v4/letter/s/eb8c5e/32.png) [@Sashen123](https://gromacs.bioexcel.eu/u/Sashen123)\ **Post date:** [September 4, 2024, 6:59am UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-is-stuck-at-step-0/7185/17 "2024-09-04T06:59:41Z")
![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/0/0b7cfae25baa8692811b93bd46cac537c64f8925.jpeg) red indicates the atom. this case its atom 185 error is posted below Steepest Descents: Tolerance (Fmax) = 2.00000e+00 Number of steps = 50000 Step= 0, Dmax= 1.0e-02 nm, Epot= 4.68220e+35 Fmax= inf, atom= 185 # =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = RANK 0 PID 200942 RUNNING AT gphnode003 = KILLED BY SIGNAL: 9 (Killed) =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = RANK 1 PID 200943 RUNNING AT gphnode003 = KILLED BY SIGNAL: 11 (Segmentation fault) ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [September 4, 2024, 7:17am UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-is-stuck-at-step-0/7185/18 "2024-09-04T07:17:49Z")
Thanks. So far, I agree, nothing looks strange. Can you post an image of the periodic representations in the Z dimension as well? Are you using restraints in the EM? If so, is the restraint reference similar to the starting configuration? ---
**Author:** ![Sashen123](https://avatars.discourse-cdn.com/v4/letter/s/eb8c5e/32.png) [@Sashen123](https://gromacs.bioexcel.eu/u/Sashen123)\ **Post date:** [September 4, 2024, 3:33pm UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-is-stuck-at-step-0/7185/19 "2024-09-04T15:33:17Z")
![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/6/6d755ed655721ebb9ffbe867358fcf163d411729.jpeg) Nope I am not using any restraints. The mdp inputs are posted below. integrator = steep emtol = 2.0 emstep = 0.01 nsteps = 50000 nstlist = 20 cutoff-scheme = Verlet ns\_type = grid coulombtype = PME rcoulomb = 1.4 rvdw = 1.4 pbc = xyz ---
**Author:** ![Sashen123](https://avatars.discourse-cdn.com/v4/letter/s/eb8c5e/32.png) [@Sashen123](https://gromacs.bioexcel.eu/u/Sashen123)\ **Post date:** [September 4, 2024, 3:38pm UTC](https://gromacs.bioexcel.eu/t/gmx-mdrun-is-stuck-at-step-0/7185/20 "2024-09-04T15:38:28Z")
I believe the parameters are correct (Used OPLS) since I can run randomly packed configurations and single molecule simulations. [Next page](https://gromacs.bioexcel.eu/t/gmx-mdrun-is-stuck-at-step-0/7185.md?page=2)