Force field in the GROMACS topology format to LAMMPS format

LAMMPS LAMMPS General Discussion
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1

Dear All,

How do I convert this Ethylene glycol topology and parameter set in GROMACS format to LAMMPS format?

The set was obtained from this paper https://doi.org/10.1021/jp109914s

#define _FF_OPLS
#define _FF_OPLSAA

[ defaults ]
; nbfunc    comb-rule   gen-pairs   fudgeLJ fudgeQQ
       1            3         yes       0.5     0.5

[ atomtypes ]
; name  bond_type      mass    charge   ptype          sigma      epsilon
    CG      CG  6  12.01100    0.1650       A    3.50000e-01  2.76144e-01
    HG      HG  1   1.00800    0.0600       A    2.50000e-01  1.25520e-01
    OG      OG  8  15.99940   -0.7200       A    3.00000e-01  7.11280e-01
    HO      HO  1   1.00800    0.4350       A    0.00000e+00  0.00000e+00

[ bondtypes ]
;  i     j   func         b0         kb
  CG    CG      1    0.15290   224262.0
  CG    HG      1    0.10900   284512.0
  CG    OG      1    0.14300   267776.0
  OG    HO      1    0.09450   462750.4

[ angletypes ]
;  i     j     k   func      th0      cth
  CG    CG    OG      1   108.00   418.40
  CG    CG    HG      1   110.70   313.80
  HG    CG    HG      1   107.80   276.14
  HG    CG    OG      1   109.50   292.88
  CG    OG    HO      1   108.50   460.24

[ dihedraltypes ]
;   i    j     k     l   func  coefficients
   OG    CG    CG    OG  3    9.852  11.989   4.987 -26.828   0.000   0.000
   CG    CG    OG    HO  3   -0.141   5.591   3.156  -8.606   0.000   0.000

; Fourier coefficients
; angle    F1      F2      F3
; OCCO   16.264  -4.987  13.414
; CCOH    1.727  -3.156   4.303

Best regards,
Yunes Salman

2
  • Look up the syntax of the itp files in Gromacs in the Gromacs documentation So you know which value means what
  • Also find out which units settings Gromacs uses (I think it is kJ/mole and nanometers, but you better make certain)
  • Look up what potential functions are used by OPLS/AA in Gromacs and then find their equivalent in LAMMPS
  • Convert all settings and parameters to the equivalent in LAMMPS
1 Like
3

If you are planning to work with organic materials, I suggest giving a go to Moltemplate. It is a scripting language to render LAMMPS-template (LT) files into a working input deck. It has useful functions, like combining a structure file (DUMP, PDB, XYZ) with the force field describing individual molecules. It ships an oplsaa.lt file with the whole force field and settings.

Here an example of a simple molecule, formamide, written in the LT format:

import "/usr/local/moltemplate/moltemplate/force_fields/oplsaa.lt"

# The "oplsaa.lt" file contains force-field parameters, atom type definitions,
# partial charges, masses and bond-angle rules for the atoms in your system.

_FAM inherits OPLSAA {

  # atom-id mol-id atom-type charge   X       Y       Z     # comment

  write('Data Atoms') {
    $atom:C00 $mol @atom:177  0.00  0.100014490    0.490422099    0.0
    $atom:O01 $mol @atom:178  0.00  1.091153187   -0.250749643    0.0
    $atom:N02 $mol @atom:179  0.00 -1.121616690   -0.181085754    0.0
    $atom:H03 $mol @atom:182  0.00 -2.013715893    0.272535813    0.0
    $atom:H04 $mol @atom:182  0.00 -1.056768463   -1.190185868    0.0
    $atom:H05 $mol @atom:221  0.00  0.144676387    1.570292021    0.0
  }

  # Note: You don't have to specify the charge in this example because we are
  #       using the OPLSAA force-field which assigns charge according to
  #       atom-type.  Just leave these numbers as 0.00 for now.
  # Note: LAMMPS expects an integer in the 2nd column (the Molecule-ID number).
  #       If we put "$mol" there, moltemplate will generate this integer for you

  # A list of the bonds in the molecule:
  # BondID     AtomID1  AtomID2

  write('Data Bond List') {
    $bond:C1 $atom:C00 $atom:O01
    $bond:C2 $atom:C00 $atom:H05
    $bond:C3 $atom:C00 $atom:N02
    $bond:C4 $atom:N02 $atom:H03
    $bond:C5 $atom:N02 $atom:H04
  }

  # In the "Data Bond List" section we don't have to specify the bond type.
  # The bond-type will be determined by the atom type (according to "oplsaa.lt")

}

This is technically a forum for LAMMPS, but I believe that MOLTEMPLATE really unleashes the true potential of LAMMPS by rendering complex structures into perfect data and input files. Good luck!

2 Likes
4

Thank you very much for this tip. I used Moltemplate before but I didn’t know about this function.