Help request protein-ligand tutorial error fix

pmx
1

Request help to fix this in some detail.
I was following the tutorial: ligand_tutorial
At the step doing eq_nvt, I believe I am encountering two errors.
I do not know how to fix this and move forward. I am enclosing the details below (after ******).
Error1 (?): ‘Update groups can not be used for this system because an incompatible virtual site type is used’
Error2: ‘Fatal error:’
‘There is no domain decomposition for 20 ranks that is compatible with the’
‘given box and a minimum cell size of 0.94825 nm’

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

Run simulation locally: eq_nvt

Running: LIG edge_18625-1_18626-1 stateA run1
b’ :slight_smile: GROMACS - gmx mdrun, 2023.3-Ubuntu_2023.3_1ubuntu3 (-:’
b’’
b’Executable: /usr/bin/gmx’
b’Data prefix: /usr’
b’Working dir: /mnt/g/GROMACS/pmx’
b’Command line:’
b’ gmx mdrun -s /mnt/g/GROMACS/pmx/workpath/edge_18625-1_18626-1/water/stateA/run1/eq_nvt/tpr.tpr -e /mnt/g/GROMACS/pmx/workpath/edge_18625-1_18626-1/water/stateA/run1/eq_nvt/ener.edr -c /mnt/g/GROMACS/pmx/workpath/edge_18625-1_18626-1/water/stateA/run1/eq_nvt/confout.gro -x /mnt/g/GROMACS/pmx/workpath/edge_18625-1_18626-1/water/stateA/run1/eq_nvt/traj_comp.xtc -o /mnt/g/GROMACS/pmx/workpath/edge_18625-1_18626-1/water/stateA/run1/eq_nvt/traj.trr -cpo /mnt/g/GROMACS/pmx/workpath/edge_18625-1_18626-1/water/stateA/run1/eq_nvt/state.cpt -g /mnt/g/GROMACS/pmx/workpath/edge_18625-1_18626-1/water/stateA/run1/eq_nvt/md.log -dhdl /mnt/g/GROMACS/pmx/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/GROMACS/pmx/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’

2

Hi,

We’ve modified the tutorial and now you can change the rank with “-ntomp” flag. You can modify the default ntomp=‘8’ to others (‘4’ or ‘16’, …) if you like in the fe.run_simulation_locally( simType=‘em’, bProt=False, ntomp=‘8’, bVerbose=True ) step. The default should also work fine.

Please use the updated tutorial from here: ligand_tutorial

Thanks,
Sudarshan

3

Request Clarification: tutorial ligand_tutorial
I observe at nvt step: fe.prepare_simulation( simType=‘eq_nvt’, bProt=True)
[please review the terminal output…]Getting:
Fatal error:
number of coordinates in coordinate file
(/mnt/g/pmxvnb/tutorial_files/workpath/edge_18625-1_18626-1/protein/stateA/run1/em/confout.gro,
71537)
does not match topology
(/mnt/g/pmxvnb/tutorial_files/workpath/edge_18625-1_18626-1/water/topol.top,
5605)
The generated gmx grompp is as follows:
gmx grompp
-f /mnt/g/pmxvnb/tutorial_files/input/mdppath/eq_nvt_l0.mdp
-c /mnt/g/pmxvnb/tutorial_files/workpath/edge_18625-1_18626-1/protein/stateA/run1/em/confout.gro
-r /mnt/g/pmxvnb/tutorial_files/workpath/edge_18625-1_18626-1/protein/stateA/run1/em/confout.gro
-p /mnt/g/pmxvnb/tutorial_files/workpath/edge_18625-1_18626-1/water/topol.top
-o /mnt/g/pmxvnb/tutorial_files/workpath/edge_18625-1_18626-1/protein/stateA/run1/eq_nvt/tpr.tpr
-maxwarn 4
-po /mnt/g/pmxvnb/tutorial_files/workpath/edge_18625-1_18626-1/protein/stateA/run1/eq_nvt/mdout.mdp

It is observed for protein “water/topl.top” used which is giving fatal error. HOW TO CORRECT THIS IN THE SCRIPT. PLEASE HELP

4

Hi,

Thanks for pointing out the issue.

It’s resolved now. It should run fine if you start the tutorial from the beginning again.

Thanks