GMDFF

1.2. GMDFF#

1.2.1. MD Force Fields#

The GMDFF module mediates the creation of force field parameters (itp files), as well as making special adjustments for the construction of the topology (top file). The simplest usage consists of the following command:

gmdff ⟨input.ext⟩

where ext is one of the extensions recognized by the Solvate Suite (com/log [Gaussian], inp/out [ORCA], xyz/xtb [xTB], gro/pdb [GROMACS]).

Note

Simply type gmdff in the terminal and press enter to see the full list of execution options for the module.

If the simulation box is prepared for the GROMACS program (which is determined by the extension of the input files) the program automatically runs the GMDFF module, which prepares the force field files as well as the system topology file. This means that, in the general case, it is possible to create the simulation box and its topology file from a single command line. In these cases, however, it is recommended to run the GMDFF module first, in order to prepare all the necessary force field files required for executing the PACKS module. This is done using the following command structure:

gmdff ⟨input.ext⟩ [⟨-options⟩]

where ext is one of the extensions recognized by Solvate Suite (com/log [Gaussian], inp/out [ORCA], xyz/xtb [xTB], gro/pdb [GROMACS]), input is the file with the structure of the solute or solvent molecule, and “-options” a set of options for the configuration of the force field to be created.

There are 4 scenarios in which this module can be used:

  • In the case of biomolecule PDB files, the program performs structure preparation (removal of heteroatoms and addition of hydrogens, without adjusting protonation based on pH, which may require additional preparations to be carried out by the user), followed by conversion to the GROMACS format (gro file) and creation of the force field parameters in a single input (itp file).

  • In the case of force fields obtained by external servers (such as LigParGen and ATB) the module removes any residual charges, a necessary step for building simulation boxes that are, in fact, electrically neutral. This is done by homogeneously compensating for any residual charge between all atoms in the structure.

  • In the case of internally parameterized solvent molecules, the program selects the appropriate parameters and writes them to a force field input (itp file), as well as converting the input file to the appropriate format (gro file).

  • In the case of small molecules, the module sequentially executes the Q-Force program to generate parameters from a quantum chemical calculation.

Note

In the case of using the Q-Force program, the user can generate a default settings file with the -chk option. The edited file can then be read by the program with the -cfg option. Alternatively, the user can provide his own settings file with the -cfg ⟨file.ini⟩ command.

For Q-Force, it is possible to check whether the options are appropriate to start the force field creation:

gmdff ⟨input.ext⟩ -chk

In this case, a configuration file (ini) is generated with a default set of execution options, which can be edited by the user to apply custom configurations. This file can then be read using the following command:

gmdff ⟨input.ext⟩ -cfg

Alternatively, the user can provide a custom settings file via the following command:

gmdff ⟨input.ext⟩ -cfg config.ini

Several force field parameters (OPLS/AA, GROMOS, CHARMM and AMBER) for a wide range of solvents are part of the program database, coming from several sources (GROMACS repository, LigParGen, ATB and Q-Force). The complete list of parameters can be displayed from the command:

gmdff -lst

It is possible to display only the parameters of a specific force field, such as OPLS/AA:

gmdff -lst opls

Once you have identified the desired parameters, you can obtain them from the command:

gmdff ⟨solvent_forcefield⟩

For example, the TIP3P parameters in the OPLS/AA force field are obtained from:

gmdff tip3p_oplsaa.wtr

Finally, if the input file matches that of the simulation box, the program combines the force field files into a single and independent topology file. This results in only two files for starting the simulation: the simulation box (gro file) and the topology (top file, with all the force field parameters).

1.2.2. Execution Options#

gmdff ⟨molecule.ext⟩ [⟨-options⟩]

  -------------------------------------------------------------------------------------------------
     .ext = Input file extension (.com/log/inp/out/xyz/xtb/pdb/gro)
          + ----------------------------------------------------------
          ● Q-Force Options
     -chr = Molecular charge.                                          [Default: 0]                [-cm][-chrg]
     -mul = Molecular multiplicity.                                    [Default: 1]                [-ml][-mult]
     -pcm = Solvent for C-PCM model.                                   [Default: None]             [-sv][-cpcm]
     -chk : Verify generated configuration file before submit.         [Default: No]               [-ck][-check]
     -cfg = Execute with user defined input configurations.            [Default: No]               [-ic][-incfg]
     -prc = Number of processors to be used.                           [Default: 4]                [-pc][-proc]
     -mem = Amount of memory in GB to be used.                         [Default: 8]                [-me][-nmem]

          ● Additional Options
     -fld = Force field parameters.      [OPL|GRO|CHM|AMB|LPG|QFC|ATB] [Default: OPLS/AA]          [-ff][-field]
     -wtr = Water model (conditional).   [SPC|SPCE||TIP3P|TIP4P|TIP5P] [Default: SPC/E]            [-wm][-water]⁽†⁾
     -lst : Provides the complete list of parameterized solvents.      [Default: No]               [-ls][-lists]
     -for : Execute in forced mode.                                    [Default: No]               [-fm][-force]
  -------------------------------------------------------------------------------------------------
  Total CPUs: 12 (max. MPI-procs.) :: System Memory: 5 GB
  -------------------------------------------------------------------------------------------------
  ⁽†⁾ Specifies the model to use if the input file corresponds to a water molecule.
  ⁽*⁾ Repositories: https://traken.chem.yale.edu/ligpargen
                    https://atb.uq.edu.au
                    https://cgenff.com

1.2.3. Quickstart Examples#

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