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.

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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

Thanks!

Galaxy Tool ID:
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2020.4+galaxy0

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 ./top_input.top -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 (-:

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and the project leaders:
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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:0,PME:0
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
                     1d01h23:33
             (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

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Hi @asif0067

Thanks for providing the details. You are using the most current tool version at UseGalaxy.eu. 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 UseGalaxy.eu 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?

Regards.

Ok. I am submitting again.

Resubmissited
Galaxy Tool ID: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2020.4+galaxy1

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' ./top_input.top &&  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 ./top_input.top -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,

Simon

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

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