gmx2qmmm

This project is maintained by gmx2qmmm

Startup example : glycine serine (GLYSER)

Glycine serine (GLYSER) includes 21 atoms. In this case, we select the first 7 atoms in the QM region and other atoms are in MM region. The figure is showed below.

alt text

Examples in example/sp and example/opt

Before running the calculation, please setup paths of the Gromacs and Gaussian

Processes from the beginning and customize names of input files

Reference to input files

  1. Prepare Coordinate file (.g96 or .gro) and Topology (.top) files of GLYSER.
  2. Create QM atom file (.ndx): Since we select the first 7 atoms in the QM region, set QM atom file (.ndx) 
     1 2 3 4 5 6 7
  3. Create QM parameters (.dat): The total chages of QM region is 1, so set the parameter charge=1 in QM parameters (.dat). Others are maintained as default. 
     charge=1
  4. Create MM parameters (.dat): We use default setting in MM parameters (.dat), so keep it empty.
  5. Create QM/MM parameters (.dat): If we run
    • a SP calculation (default setting), keep QM/MM parameters (.dat) empty.
    • a OPT calculation, set parameter jobtype=OPT in QM/MM parameters (.dat) 
        jobtype=OPT
    • a Linear SCAN calculation, set parameter jobtype=SCAN in QM/MM parameters (.dat) 
        jobtype=SCAN
      • Create a scan file scan.txt, for example: Linear scan atom1 and atom2 by 3 steps with 0.1 stepsize 
          R 1 2 0.1 3
  6. Create Path file (.dat): Setup your software path in Path file (.dat)
  7. Create Active atoms (.ndx): Select active atoms in the calculation, in this case we select all. So set Active atoms (.ndx), 
     1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
  8. Run 
     python [path of gmx2qmmm.py ][-h] [-c COORD] [-p TOP] [-n QMATOMS] [-qm QMFILE] [-mm MMFILE] [-qmmm QMMMFILE] [-act ACT] [-path PATHFILE] [-g LOGFILE]

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