Tool error in protein-ligand md simulation in Gromacs

Md simulation stopped suddenly and xtc file have not been produced. I restarted several times but got same error. Please suggest me to overcome this error.

1 Like

Hi @asif0067

This is how to start investigating why an error is occurring: Galaxy Training!

If you are not sure how to interpret the error, please post back:

  1. Server URL where you are working
  2. Full tool name and version
  3. The error message details, including the stderr and stdout


Galaxy Tool ID:

Tool error
An error occurred with this dataset:
Remote job server indicated a problem

GROMACS: gmx grompp, version 2020.4
Executable: /data/share/tools/_conda/envs/__gromacs@2020.4/bin.AVX2_256/gmx
Data prefix: /data/share/tools/_conda/envs/__gromacs@2020.4
Working dir: /data/share/staging/26133001/working
Command line:
gmx grompp -f ./md.mdp -c ./inp.gro -r ./inp.gro -n ./index.ndx -p ./ -o outp.tpr

Ignoring obsolete mdp entry ‘title’
Ignoring obsolete mdp entry ‘ns_type’
Setting the LD random seed to -1827399811
Generated 2926 of the 2926 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2926 of the 2926 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’
Excluding 3 bonded neighbours molecule type ‘UNL’
Excluding 2 bonded neighbours molecule type ‘SOL’
Excluding 1 bonded neighbours molecule type ‘NA’
Number of degrees of freedom in T-Coupling group Protein_UNL is 8336.85
Number of degrees of freedom in T-Coupling group Water_and_ions is 153435.16
Estimate for the relative computational load of the PME mesh part: 0.15

NOTE 1 [file ./md.mdp]:
This run will generate roughly 3862 Mb of data

There was 1 note

GROMACS reminds you: “Try to calculate the numbers that have been” (The Smoke Fairies)

turning H bonds into constraints…
turning H bonds into constraints…
turning H bonds into constraints…
turning H bonds into constraints…
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K
Calculated rlist for 1x1 atom pair-list as 1.297 nm, buffer size 0.097 nm
Set rlist, assuming 4x4 atom pair-list, to 1.224 nm, buffer size 0.024 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 60x60x60, spacing 0.156 0.156 0.156
:slight_smile: GROMACS - gmx mdrun, 2020.4 (-:

                        GROMACS is written by:
 Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    

Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS: gmx mdrun, version 2020.4
Executable: /data/share/tools/_conda/envs/__gromacs@2020.4/bin/gmx_gpu
Data prefix: /data/share/tools/_conda/envs/__gromacs@2020.4
Working dir: /data/share/staging/26133001/working
Command line:
gmx_gpu mdrun -ntmpi 1 -nb gpu -pme gpu -nt 8 -deffnm outp

Reading file outp.tpr, VERSION 2020.4 (single precision)
Changing nstlist from 20 to 100, rlist from 1.224 to 1.345

1 GPU selected for this run.
Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:
PP tasks will do (non-perturbed) short-ranged interactions on the GPU
PP task will update and constrain coordinates on the CPU
PME tasks will do all aspects on the GPU
Using 1 MPI thread

Non-default thread affinity set, disabling internal thread affinity

Using 8 OpenMP threads

WARNING: This run will generate roughly 3843 Mb of data

starting mdrun ‘Protein-Ligand in water’
50000000 steps, 100000.0 ps.

Writing final coordinates.

           Core t (s)   Wall t (s)        (%)
   Time:   731308.351    91413.557      800.0
             (ns/day)    (hour/ns)

Performance: 94.516 0.254

Thanx for Using GROMACS - Have a Nice Day

title = Protein-ligand complex MD simulation
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000000 ; 2 * 50000000 = 100000 ps (100 ns)
dt = 0.002 ; 2 fs
; Output control
nstenergy = 5000 ; save energies every 10.0 ps
nstlog = 5000 ; update log file every 10.0 ps
nstxout-compressed = 5000 ; save coordinates every 10.0 ps
; Bond parameters
continuation = yes ; continuing from NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds to H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighbor searching and vdW
cutoff-scheme = Verlet
ns_type = grid ; search neighboring grid cells
nstlist = 20 ; largely irrelevant with Verlet
rlist = 1.2
vdwtype = cutoff
vdw-modifier = force-switch
rvdw-switch = 1.0
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
rcoulomb = 1.2
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein_UNL Water_and_ions ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 310 310 ; reference temperature, one for each group, in K
; Pressure coupling
pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction is not used for proteins with the C36 additive FF
DispCorr = no
; Velocity generation
gen_vel = no ; continuing from NPT equilibration

1 Like

Hi @asif0067

Thanks for providing the details. You are using the most current tool version at The job appears to be running out of resources during execution (~4 GB of data is very large for any public Galaxy server to process).

Please submit a bug report for this error and include a link to this topic in the comments. The admin/support team should be able to help you more. My guess is that the job will be too large as is, but they can confirm.

cc @bjoern.gruening @wm75 @gallardoalba

Tutorial: Running molecular dynamics simulations using GROMACS

I reported for this error but there is no reply from chemoinformatics expert via emails.

I restarted several times but no xtc file was generated so failed again and again. Please solve this issue.

Hi @asif0067,
I have checked the error reports, but didn’t find the one corresponding to GROMACS. Could you try to submit it once again?


Ok. I am submitting again.

Galaxy Tool ID:

Job API ID: 11ac94870d0bb33a89cd26bce070f612

Command Line:

ln -s '/data/share/staging/29031595/inputs/dataset_a5b73911-0cc4-4c57-9630-499070226db9.dat' ./md.mdp &&  ln -s '/data/share/staging/29031595/inputs/dataset_230c9ef5-e546-409d-8892-4eeb8d0b3d56.dat' ./inp.gro && ln -s '/data/share/staging/29031595/inputs/dataset_9f6e79c1-e1d4-44e8-b298-038bb5270172.dat' ./ &&  ln -s '/data/share/staging/29031595/inputs/dataset_0f7fbca9-2d70-481e-97f9-b4ec87c48209.dat' ./posres.itp &&   ln -s '/data/share/staging/29031595/inputs/dataset_3bfdfcae-8ae2-4b71-9f1c-08bf1016052a.dat' ./index.ndx &&  gmx grompp -f ./md.mdp -c ./inp.gro -r ./inp.gro -n ./index.ndx -p ./ -o outp.tpr &>> verbose.txt &&  gmx mdrun -nt "${GALAXY_SLOTS:-4}" -deffnm outp &>> verbose.txt   && cat md.mdp &>> verbose.txt

Please check it

Sorry, we haven’t got any report. Have you used the bug icon?

Screenshot from 2021-08-30 10-55-07

Yes I used this icon to submit the error in the beginning of this occurence

I tried rerunning your job, just changing the number of steps to 500, and it completed without any error. So the problem doesn’t appear to be on the GROMACS side.

I don’t have any helpful suggestion, but I recommend you use your own resources for conducting these kind of simulations.

All the best,


1 Like

But previous runs having 50000000 steps which were completed successfully. So whats the problem about these new run same as before?

1 Like