Installation Problem of PMX

vnbalaji · November 8, 2024, 7:50am

I am encountering the following error during installation of pmx in conda. Please suggest solution. Thanks. Balaji. Requirement already satisfied: six>=1.5 in c:\programdata\anaconda3\envs\pmx\lib\site-packages (from python-dateutil>=2.7->matplotlib->pmx==0+untagged.886.ge6d6258) (1.16.0)
Building wheels for collected packages: pmx
Building wheel for pmx (setup.py) … error
error: subprocess-exited-with-error

× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [663 lines of output]
C:\ProgramData\anaconda3\envs\PMX\lib\site-packages\setuptools_init_.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
!!

          ********************************************************************************
          Requirements should be satisfied by a PEP 517 installer.
          If you are using pip, you can try `pip install --use-pep517`.
          ********************************************************************************

  !!
    dist.fetch_build_eggs(dist.setup_requires)
  running bdist_wheel

Sudchem · November 8, 2024, 12:08pm

Hi,

Are you following the installation steps described here (pmx/tutorials/INSTALL at develop · deGrootLab/pmx · GitHub)?

vnbalaji · November 8, 2024, 12:37pm

Thank you Sudarshan for your kind reply.
I followed the steps outlined as per the link.
One question: I have installed the Anaconda in Windows11 and used the conda prompt and created the environment and installed as per instruction.
Is this ok. or I have to install all these in ubuntu or other unix platforms? Kindly advise.
Thanks and regards
Balaji

Sudchem · November 8, 2024, 5:14pm

Hi Balaji,

We have never tested pmx (or gromacs) installation in Windows.
It works properly in linux systems.
So, if possible I would suggest to use linux.

Thanks,
Sudarshan

vnbalaji · November 9, 2024, 12:52am

Thank you for your input Sudarshan. I will try the Linux system.
Balaji

vnbalaji · November 19, 2024, 1:09am

I was able to install pmx successfully in Ubuntu. Thanks. I am trying to run ligand tutorials. I followed the tutorials as described in the video link: https://www.youtube.com/watch?v=NSeiQUwc8-I&t=281s I am able to run upto step 7. Please let me know what I should do for the error I am encountering in step 9 I get the error:
Error in user input:
Invalid command-line options
In command-line option -c
File
‘/home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/protein/stateB/run3/em/confout.gro’
does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
In command-line option -r
File
‘/home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/protein/stateB/run3/em/confout.gro’
does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)

Sudchem · November 19, 2024, 6:19am

Hi Balaji,

It’s clear from the error message, “File
‘/home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/protein/stateB/run3/em/confout.gro’
does not exist or is not accessible”.
Either your energy minimization (em) was not successfully finished or the path is wrong.

Best,
Sudarshan

vnbalaji · November 22, 2024, 3:10pm

IN THE TUTORIAL-WHEN I AM EXECUTING THE STEP locally:

fe.run_simulation_locally( simType=‘em’, bProt=False, bVerbose=True )

I GET THE FOLLOWING output. THIS CONTAINS confout.gro for /water/ State A and B for run1, run2 and run3.
I do not see any /protein/ output which is required in the next step. kindly let me
know what is that i am doing wrong. Please help. Balaji.

------------------------output-------------------
Run simulation locally: em

Running: LIG edge_18625-1_18626-1 stateA run1
b’ GROMACS - gmx mdrun, 2023.3-Ubuntu_2023.3_1ubuntu3 (-:’
b’’
b’Executable: /usr/bin/gmx’
b’Data prefix: /usr’
b’Working dir: /home/vnbalaji/pmx/tutorials’
b’Command line:’
b’ gmx mdrun -s /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run1/em/tpr.tpr -e /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run1/em/ener.edr -c /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run1/em/confout.gro -o /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run1/em/traj.trr -g /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run1/em/md.log’
b’’
b’’
b’Back Off! I just backed up /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run1/em/md.log to /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run1/em/#md.log.1#’
b’Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log).’
b’Reading file /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run1/em/tpr.tpr, VERSION 2023.3-Ubuntu_2023.3_1ubuntu3 (single precision)’
b’Update groups can not be used for this system because an incompatible virtual site type is used’
b’’
b’Using 28 MPI threads’
b’Using 1 OpenMP thread per tMPI thread’
b’’
b’’
b’Back Off! I just backed up /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run1/em/traj.trr to /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run1/em/#traj.trr.1#’
b’’
b’Back Off! I just backed up /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run1/em/ener.edr to /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run1/em/#ener.edr.1#’
b’’
b’Steepest Descents:’
b’ Tolerance (Fmax) = 1.00000e+02’
b’ Number of steps = 10000’
b’’
b’Energy minimization reached the maximum number of steps before the forces’
b’reached the requested precision Fmax < 100.’
b’’
b’writing lowest energy coordinates.’
b’’
b’Back Off! I just backed up /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run1/em/confout.gro to /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run1/em/#confout.gro.1#’
b’’
b’Steepest Descents did not converge to Fmax < 100 in 10001 steps.’
b’Potential Energy = -1.0085691e+05’
b’Maximum force = 9.8876727e+02 on atom 9’
b’Norm of force = 1.6075598e+01’
b’’
b’GROMACS reminds you: “If Java had true garbage collection, most programs would delete themselves upon execution.” (Robert Sewell)’
b’’
Running: LIG edge_18625-1_18626-1 stateA run2
b’ GROMACS - gmx mdrun, 2023.3-Ubuntu_2023.3_1ubuntu3 (-:’
b’’
b’Executable: /usr/bin/gmx’
b’Data prefix: /usr’
b’Working dir: /home/vnbalaji/pmx/tutorials’
b’Command line:’
b’ gmx mdrun -s /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run2/em/tpr.tpr -e /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run2/em/ener.edr -c /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run2/em/confout.gro -o /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run2/em/traj.trr -g /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run2/em/md.log’
b’’
b’’
b’Back Off! I just backed up /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run2/em/md.log to /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run2/em/#md.log.1#’
b’Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log).’
b’Reading file /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run2/em/tpr.tpr, VERSION 2023.3-Ubuntu_2023.3_1ubuntu3 (single precision)’
b’Update groups can not be used for this system because an incompatible virtual site type is used’
b’’
b’Using 28 MPI threads’
b’Using 1 OpenMP thread per tMPI thread’
b’’
b’’
b’Back Off! I just backed up /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run2/em/traj.trr to /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run2/em/#traj.trr.1#’
b’’
b’Back Off! I just backed up /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run2/em/ener.edr to /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run2/em/#ener.edr.1#’
b’’
b’Steepest Descents:’
b’ Tolerance (Fmax) = 1.00000e+02’
b’ Number of steps = 10000’
b’’
b’Energy minimization reached the maximum number of steps before the forces’
b’reached the requested precision Fmax < 100.’
b’’
b’writing lowest energy coordinates.’
b’’
b’Back Off! I just backed up /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run2/em/confout.gro to /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run2/em/#confout.gro.1#’
b’’
b’Steepest Descents did not converge to Fmax < 100 in 10001 steps.’
b’Potential Energy = -1.0085362e+05’
b’Maximum force = 1.1962727e+03 on atom 9’
b’Norm of force = 1.9068720e+01’
b’’
b’GROMACS reminds you: “Can someone please tell Icarus that he's not the only one falling from the sky?” (Urban Dance Squad)’
b’’
Running: LIG edge_18625-1_18626-1 stateA run3
b’ GROMACS - gmx mdrun, 2023.3-Ubuntu_2023.3_1ubuntu3 (-:’
b’’
b’Executable: /usr/bin/gmx’
b’Data prefix: /usr’
b’Working dir: /home/vnbalaji/pmx/tutorials’
b’Command line:’
b’ gmx mdrun -s /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run3/em/tpr.tpr -e /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run3/em/ener.edr -c /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run3/em/confout.gro -o /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run3/em/traj.trr -g /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run3/em/md.log’
b’’
b’’
b’Back Off! I just backed up /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run3/em/md.log to /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run3/em/#md.log.1#’
b’Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log).’
b’Reading file /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run3/em/tpr.tpr, VERSION 2023.3-Ubuntu_2023.3_1ubuntu3 (single precision)’
b’Update groups can not be used for this system because an incompatible virtual site type is used’
b’’
b’Using 28 MPI threads’
b’Using 1 OpenMP thread per tMPI thread’
b’’
b’’
b’Back Off! I just backed up /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run3/em/traj.trr to /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run3/em/#traj.trr.1#’
b’’
b’Back Off! I just backed up /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run3/em/ener.edr to /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run3/em/#ener.edr.1#’
b’’
b’Steepest Descents:’
b’ Tolerance (Fmax) = 1.00000e+02’
b’ Number of steps = 10000’
b’’
b’Energy minimization reached the maximum number of steps before the forces’
b’reached the requested precision Fmax < 100.’
b’’
b’writing lowest energy coordinates.’
b’’
b’Back Off! I just backed up /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run3/em/confout.gro to /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateA/run3/em/#confout.gro.1#’
b’’
b’Steepest Descents did not converge to Fmax < 100 in 10001 steps.’
b’Potential Energy = -1.0085393e+05’
b’Maximum force = 6.3011346e+02 on atom 9’
b’Norm of force = 1.1120519e+01’
b’’
b’GROMACS reminds you: “Is This the Right Room for an Argument ?” (Monty Python)’
b’’
Running: LIG edge_18625-1_18626-1 stateB run1
b’ GROMACS - gmx mdrun, 2023.3-Ubuntu_2023.3_1ubuntu3 (-:’
b’’
b’Executable: /usr/bin/gmx’
b’Data prefix: /usr’
b’Working dir: /home/vnbalaji/pmx/tutorials’
b’Command line:’
b’ gmx mdrun -s /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run1/em/tpr.tpr -e /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run1/em/ener.edr -c /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run1/em/confout.gro -o /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run1/em/traj.trr -g /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run1/em/md.log’
b’’
b’’
b’Back Off! I just backed up /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run1/em/md.log to /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run1/em/#md.log.1#’
b’Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log).’
b’Reading file /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run1/em/tpr.tpr, VERSION 2023.3-Ubuntu_2023.3_1ubuntu3 (single precision)’
b’Update groups can not be used for this system because an incompatible virtual site type is used’
b’’
b’Using 28 MPI threads’
b’Using 1 OpenMP thread per tMPI thread’
b’’
b’’
b’Back Off! I just backed up /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run1/em/traj.trr to /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run1/em/#traj.trr.1#’
b’’
b’Back Off! I just backed up /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run1/em/ener.edr to /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run1/em/#ener.edr.1#’
b’’
b’Steepest Descents:’
b’ Tolerance (Fmax) = 1.00000e+02’
b’ Number of steps = 10000’
b’’
b’Energy minimization reached the maximum number of steps before the forces’
b’reached the requested precision Fmax < 100.’
b’’
b’writing lowest energy coordinates.’
b’’
b’Back Off! I just backed up /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run1/em/confout.gro to /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run1/em/#confout.gro.1#’
b’’
b’Steepest Descents did not converge to Fmax < 100 in 10001 steps.’
b’Potential Energy = -1.0085503e+05’
b’Maximum force = 7.1137817e+02 on atom 9’
b’Norm of force = 1.2132693e+01’
b’’
b’GROMACS reminds you: “Wicky-wicky Wa-wild West” (Will Smith)’
b’’
Running: LIG edge_18625-1_18626-1 stateB run2
b’ GROMACS - gmx mdrun, 2023.3-Ubuntu_2023.3_1ubuntu3 (-:’
b’’
b’Executable: /usr/bin/gmx’
b’Data prefix: /usr’
b’Working dir: /home/vnbalaji/pmx/tutorials’
b’Command line:’
b’ gmx mdrun -s /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run2/em/tpr.tpr -e /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run2/em/ener.edr -c /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run2/em/confout.gro -o /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run2/em/traj.trr -g /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run2/em/md.log’
b’’
b’’
b’Back Off! I just backed up /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run2/em/md.log to /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run2/em/#md.log.1#’
b’Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log).’
b’Reading file /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run2/em/tpr.tpr, VERSION 2023.3-Ubuntu_2023.3_1ubuntu3 (single precision)’
b’Update groups can not be used for this system because an incompatible virtual site type is used’
b’’
b’Using 28 MPI threads’
b’Using 1 OpenMP thread per tMPI thread’
b’’
b’’
b’Back Off! I just backed up /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run2/em/traj.trr to /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run2/em/#traj.trr.1#’
b’’
b’Back Off! I just backed up /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run2/em/ener.edr to /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run2/em/#ener.edr.1#’
b’’
b’Steepest Descents:’
b’ Tolerance (Fmax) = 1.00000e+02’
b’ Number of steps = 10000’
b’’
b’writing lowest energy coordinates.’
b’’
b’Back Off! I just backed up /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run2/em/confout.gro to /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run2/em/#confout.gro.1#’
b’’
b’Steepest Descents converged to Fmax < 100 in 9483 steps’
b’Potential Energy = -1.0076638e+05’
b’Maximum force = 9.0853745e+01 on atom 9’
b’Norm of force = 5.4172597e+00’
b’’
b’GROMACS reminds you: “There's a limit to how many times you can read how great you are and what an inspiration you are, but I'm not there yet.” (Randy Pausch)’
b’’
Running: LIG edge_18625-1_18626-1 stateB run3
b’ GROMACS - gmx mdrun, 2023.3-Ubuntu_2023.3_1ubuntu3 (-:’
b’’
b’Executable: /usr/bin/gmx’
b’Data prefix: /usr’
b’Working dir: /home/vnbalaji/pmx/tutorials’
b’Command line:’
b’ gmx mdrun -s /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run3/em/tpr.tpr -e /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run3/em/ener.edr -c /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run3/em/confout.gro -o /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run3/em/traj.trr -g /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run3/em/md.log’
b’’
b’’
b’Back Off! I just backed up /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run3/em/md.log to /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run3/em/#md.log.1#’
b’Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log).’
b’Reading file /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run3/em/tpr.tpr, VERSION 2023.3-Ubuntu_2023.3_1ubuntu3 (single precision)’
b’Update groups can not be used for this system because an incompatible virtual site type is used’
b’’
b’Using 28 MPI threads’
b’Using 1 OpenMP thread per tMPI thread’
b’’
b’’
b’Back Off! I just backed up /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run3/em/traj.trr to /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run3/em/#traj.trr.1#’
b’’
b’Back Off! I just backed up /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run3/em/ener.edr to /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run3/em/#ener.edr.1#’
b’’
b’Steepest Descents:’
b’ Tolerance (Fmax) = 1.00000e+02’
b’ Number of steps = 10000’
b’’
b’writing lowest energy coordinates.’
b’’
b’Back Off! I just backed up /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run3/em/confout.gro to /home/vnbalaji/pmx/tutorials/workpath/edge_18625-1_18626-1/water/stateB/run3/em/#confout.gro.1#’
b’’
b’Steepest Descents converged to Fmax < 100 in 9483 steps’
b’Potential Energy = -1.0076193e+05’
b’Maximum force = 9.9436401e+01 on atom 9’
b’Norm of force = 5.4547805e+00’
b’’
b’GROMACS reminds you: “Protons give an atom its identity, electrons its personality.” (Bill Bryson)’
b’’
DONE

Sudchem · November 22, 2024, 4:40pm

Hi Balaji,

If you want just run the tutorial, you can do “bProt=False” in your next step as well. This flag will avoid running the protein branch.

fe.prepare_simulation( simType=‘eq’ , bProt=False)

All the best

vnbalaji · November 26, 2024, 4:11pm

http://pmx.mpibpc.mpg.de/Tutorial2024/Baltic_HPC2024/ligand_tutorial.html
I was running this tutorial.
At running step:
fe.run_simulation_locally( simType=‘eq_nvt’, bProt=False, bVerbose=True )
I am encountering the following error. Kindly revert what I should do. Thanks

Run simulation locally: eq_nvt

Running: LIG edge_18625-1_18626-1 stateA run1
b’ GROMACS - gmx mdrun, 2023.3-Ubuntu_2023.3_1ubuntu3 (-:’
b’’
b’Executable: /usr/bin/gmx’
b’Data prefix: /usr’
b’Working dir: /mnt/g/VNBMD/tutorial_files’
b’Command line:’
b’ gmx mdrun -s /mnt/g/VNBMD/tutorial_files/workpath/edge_18625-1_18626-1/water/stateA/run1/eq_nvt/tpr.tpr -e /mnt/g/VNBMD/tutorial_files/workpath/edge_18625-1_18626-1/water/stateA/run1/eq_nvt/ener.edr -c /mnt/g/VNBMD/tutorial_files/workpath/edge_18625-1_18626-1/water/stateA/run1/eq_nvt/confout.gro -x /mnt/g/VNBMD/tutorial_files/workpath/edge_18625-1_18626-1/water/stateA/run1/eq_nvt/traj_comp.xtc -o /mnt/g/VNBMD/tutorial_files/workpath/edge_18625-1_18626-1/water/stateA/run1/eq_nvt/traj.trr -cpo /mnt/g/VNBMD/tutorial_files/workpath/edge_18625-1_18626-1/water/stateA/run1/eq_nvt/state.cpt -g /mnt/g/VNBMD/tutorial_files/workpath/edge_18625-1_18626-1/water/stateA/run1/eq_nvt/md.log -dhdl /mnt/g/VNBMD/tutorial_files/workpath/edge_18625-1_18626-1/water/stateA/run1/eq_nvt/dhdl.xvg’
b’’
b’Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log).’
b’Reading file /mnt/g/VNBMD/tutorial_files/workpath/edge_18625-1_18626-1/water/stateA/run1/eq_nvt/tpr.tpr, VERSION 2023.3-Ubuntu_2023.3_1ubuntu3 (single precision)’
b’Changing nstlist from 10 to 80, rlist from 1.1 to 1.231’
b’’
b’Update groups can not be used for this system because an incompatible virtual site type is used’
b’’
b’-------------------------------------------------------’
b’Program: gmx mdrun, version 2023.3-Ubuntu_2023.3_1ubuntu3’
b’Source file: src/gromacs/domdec/domdec.cpp (line 2104)’
b’MPI rank: 0 (out of 28)’
b’’
b’Fatal error:’
b’There is no domain decomposition for 20 ranks that is compatible with the’
b’given box and a minimum cell size of 0.94825 nm’
b’Change the number of ranks or mdrun option -rcon or -dds or your LINCS’
b’settings’
b’Look in the log file for details on the domain decomposition’
b’’
b’For more information and tips for troubleshooting, please check the GROMACS’
b’website at Common Errors — GROMACS webpage https://www.gromacs.org documentation’
b’-------------------------------------------------------’

Sudchem · November 27, 2024, 8:36am

Hi Balaji,

That’s a gromacs specific error related to domain decomposition.
You can reduce the number of ranks/cores to resolve this.
Also, you can find quite a few suggestions for this on gromacs forums.

All the best.

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Installation Problem of PMX

IN THE TUTORIAL-WHEN I AM EXECUTING THE STEP locally:

fe.run_simulation_locally( simType=‘em’, bProt=False, bVerbose=True )

------------------------output------------------- Run simulation locally: em

Run simulation locally: eq_nvt

Related topics

------------------------output-------------------
Run simulation locally: em