• Assuming you are in the folder MD_QM-NAMD_ORCA, open VMD on the GUI and go to Extensions -> Simulation -> QwikMD The first time VMD will ask you if you want to create the folder for QwikMD, say OK.

  • In the Browser option from QwikMD type 1QRA and then Load. Accept the automatic Atom Renaming. You will also see warnings from Structure Manipulation/Check, close this box for now (OK) we will deal with parameters later.

  • Go to Chain/Type Selection and click on the A and water option to disable it.

  • Then, in the Structure Manipulation/Check you will see the residues that are included in your current system. The important point here is the option Topologies & Parameters, if you click on it it will tell you that the residue 167 is missing some parameters for GTP. Go to the option Add Topo+Param and click on the symbol +. In the box File name write the complete path to the folder where the file toppar_all36_na_nad_ppi_gdp_gtp.str is located. Here, you change the type of GTP to hetero and click on Apply.

  • You will see a box saying that parameters for the new residue will be added to the library, say “Yes”. Say OK to the message box “Topology Added”.

  • Close the windows for QwikMD, to reset the defaults.

  • In the VMD main window go again to Extensions -> Simulation -> QwikMD

  • In the Browser option from QwikMD type 1QRA and then Load. Accept the automatic Atom Renaming. Now there shouldn’t be any comments related to Structure Manipulation/Check.

  • Go to Chain/Type Selection and click on the A and water option to disable it.

  • In the main option of QwikMD called Advanced Run, choose the MD option. Here, choose Solvent=Explicit, Minimal Box, Buffer=12A, Salt conc.=0.15mol/L, Choose Salt=NaCl.

  • In Protocol, click on MD and then on the symbol - to remove this option. Select Annealing line and change the n Steps value to 12000, and the value of Equilibration n Steps to 50000.

  • In the option Simulation Setup, click on Save. Write the name for the folder which will contain the files related to the system, here we will write “mdsim” (save the changes). Then, click on Prepare to save all required files.

  • Close VMD

  • Copy the script namd.sh to the folder mdsim/run, move to this directory and submit your script sbatch namd.sh (after fixing the project ID and reservation). When the simulation finishes, you can take a look at the equilibration trajectory vmd mdsim_QwikMD.psf Equilibration.dcd.

  • Return to the director MD_QM-NAMD_ORCA ( cd ../.. ) and open VMD. Then, Extensions -> Simulation -> QwikMD

  • In the box Load of Simulation setup section, select the file mdsim.qwikmd and open it. A message box will ask you what trajectory(ies) you want to load. Choose only Equilibration and then click on Load Simulations Last Step.

  • Select now the QM/MM option in Advanced Run.

    • For Protocol, set the number of Minimization steps to 3, Annealing to 3, Equilibration to 100 and QMMM steps to 5000.
    • In QM Regions, go to + symbol to generate a QM selection. Click on that line (which contains 1 0 0 1 none) and see that the color becomes blue. Then, select the column n Atoms to display the residues. In Atom Selection write resname GTP MG or segname AP1 and resid 16, which will give you a total charge of -1 for the QM region. Set Solvent selection to 0A. Apply the changes. A total of 67 atoms will be treated quantum mechanically.

  • For QM Options, select Set Path and type:

/software/sse2/el9_epyc9005/easybuild/prefix/software/ORCA/6.1.1-gompi-2025b-avx2/bin/orca

in the file name line.

  • In the QM Command box, delete Grid4 and change TightSCF to NOSOSCF.

  • In Simulation Setup write the name of the .qwikmd file (qmsim.qwikmd in the present case): Click on Prepare and choose Current Frame.

  • Close VMD and move to the folder qmsim/run.

  • In this folder, add the following line in the conf files in the QM related section:

qmConfigLine “%PAL NPROCS 10 END”

for instance below the line qmConfigLine “!EnGrad NOSOSCF”, to run on 10 cores in parallel mode.

  • Copy the batch job for qm simulations to this current folder (cp ../../namd_qmmm.sh) and submit the jobs with sbatch namd_qmmm.sh (change the project ID).
#!/bin/bash
#SBATCH -A naiss2026-3-418-cpu 
#SBATCH -J namdjob                             
#SBATCH -t 02:50:00                            
#SBATCH -p cpu                                 
#SBATCH -N 1
#SBATCH -n 14

# load the NAMD module                         
ml purge
ml ORCA/6.1.1-avx2
ml buildtool-easybuild/5.2.1-hpca3ef7d197 NAMD/3.0.2-multicore

namd3 +p4 QMMM-Min.conf   > output_minimization.dat

#/software/sse2/el9_epyc9005/easybuild/prefix/software/ORCA/6.1.1-gompi-2025b-avx2/bin/orca /nobackup/proj/disk/support_staff/personal/pojedama/ORCA-NAMD/qmsim/run/qmmm_exec/QMMM-Min/0/qmmm_0.input