MDRUN

2.1. MDRUN#

2.1.1. MD Execution#

The MDRUN module manages the execution of simulations, through a unified interface for the ORCA and GROMACS programs. The module can be run from the main program or directly from the command:

mdrun ⟨simbox.ext⟩ [⟨-options⟩]

where ext is one of the extensions recognized by Solvate Suite (inp [ORCA] or gro [GROMACS]), and “-options” a set of the configurations for the simulation execution.

Note

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

Note

In the case of using the GROMACS 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.mdp⟩ command.

For GROMACS, it is possible to check whether the options automatically configured after packaging are appropriate to start the simulation:

mdrun ⟨simbox.gro⟩ -chk

In this case, a configuration file (mdp) 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:

mdrun ⟨simbox.gro⟩ -cfg

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

mdrun ⟨simbox.gro⟩ -cfg config.mdp

Before starting the simulation, it is necessary to carry out an initialization step for the initial box, which includes energy minimization and box optimization. For example, to initialize the simulation box at a pressure of 1.0 bar and a temperature of 298.15 K, you can use the following command:

mdrun ⟨simbox.gro⟩ -ini -prs 1.0 -tmp 298.15

After initialization, temperature equilibration can be performed in an NVT ensemble. For example, running 1.0 ns for equilibration in the NVT ensemble can be executed with the following command:

mdrun ⟨simbox.gro⟩ -nvt -tmp 298.15 -tot 1.0

and the pressure equilibration, in an NPT ensemble, with:

mdrun ⟨simbox.gro⟩ -npt -prs 1.0 -tmp 298.15 -tot 1.0

The equilibration steps involve saving the trajectory every 100 steps (in a trr file) to conserve disk space.

Note

To assess the equilibrium, the properties acquired during the simulation can be analyzed using the DATAS module.

After achieving equilibration, the production step can proceed. In this step, the trajectory is saved at each step of the simulation (in an xtc file). Production is run with the following command:

mdrun ⟨simbox.gro⟩ -prd -prs 1.0 -tmp 298.15 -tot 5.0

Note

The trajectory extraction procedure can be performed using the DATAS module, which has several extraction filters available.

Finally, after extraction, it is possible to remove several files that are unnecessary for the final step of the microsolvation treatment, which can be done with the command:

mdrun ⟨simbox.gro⟩ -cls

2.1.2. Execution Options#

mdrun ⟨file.ext⟩ [⟨-options⟩]

  -------------------------------------------------------------------------------------------------
   ORCA/GROMACS
  -------------------------------------------------------------------------------------------------
     auto : Execute the MD simulation with automatic settings.                                     [-ma](●)(■)⁽*⁾
          » Description
            ORC: [Default: -tot = 50.0 ps (prod.) | -dts = 1.0 fs]
            GMX: [Default: -tot = 2.50 ns (prod.) | -dts = 2.0 fs]
          + ----------------------------------------------------------
  » Automation Options:
    -auto : Start MD simulation with automatic settings.                                           [-ra](●)(■)⁽*⁾
    -init : Init. energy minimization with simulation box optimization procedure.                  [-ri](●)(■)⁽*⁾
    -equi : Exec. MD equilibration procedure (with auto restart).                                  [-re](●)(■)⁽*⁾
    -prod : Exec. MD production procedure (with auto restart).                                     [-rp](●)(■)⁽*⁾
    -bomd : Run a BOMD simulation at GFN2-xTB level.                                               [-rb](●)   ⁽*⁾
  » Procedure Options:
     -min : Execute an energy minimization of the simulation box.                                  [-em](●)(■)⁽*⁾
     -opt : Execute an optimization of the simulation box.                                         [-bo](●)(■)⁽*⁾
     -nvt : Run an equilibration simulation on NVT ensamble.                                       [-nv](●)(■)⁽*⁾
     -npt : Run an equilibration simulation on NPT ensamble.                                       [-np]   (■)⁽*⁾
     -prd : Run a production simulation on NVT/NPT ensamble.                                       [-pd](●)(■)⁽*⁾
  » Settings Options:
     -met = MD simulation method (GFF|GF1|GF2).                        [Default: GFF]      [Text]  [-ms](●)
     -prs = Pressure for the MD simulation (in bar).                   [Default: 1.00]     [Real]  [-ps]   (■)
     -tcp = Time constant for pressure coupling (in ps).               [Default: 0.50]     [Real]  [-tp]   (■)
     -bar = Type of barostat pressure coupling.                        [Default: Berendsen][Text]  [-br]   (■)
            * BRDS = Berendsen | CRES = C-rescale | PARR = Parrinello  | MTTK
     -tmp = Temperature for MD simulation (in K).                      [Default: 298.15]   [Real]  [-ts](●)(■)
     -tct = Time constant for temperature coupling (in ps).            [Default: 0.50]     [Real]  [-tc]   (■)
     -ter = Type of thermostat temperature coupling.                   [Default: V-rescale][Text]  [-tr]   (■)
            * BRDS = Berendsen | VRES = V-rescale | NOSE = Nose-Hoover | ADSN = Andersen
     -kap = Isothermal compressibility value (in bar⁻¹).               [Default: 1.0E-6]   [Real]  [-kp]   (■)
     -nst = Simulation steps to update neighbor list.                  [Default: 100]      [Int.]  [-ns]   (■)
     -dmp = Number of steps for dump positions.                        [Default: 1]        [Int.]  [-dp](●)(■)
     -dts = Simulation time step (in fs).                              [Default: 1.0]      [Real]  [-dt]   (■)
     -tot = Simulation additional (ORCA) or total (GMX) time (in ps).  [Default: Automatic][Real]  [-tt](●)(■)
     -nrs = Number of simulation run steps.                            [Default: Automatic][Int.]  [-nr](●)(■)
  » Additional Options:
     -prc = Number of parallel CPU processes to run.                   [Default: 4]                [-pc](●)
     -chk : Check generated files before submit.                       [Default: No]               [-ck](●)(■)
     -cfg = Execute with user defined input configurations.            [Default: No]               [-ic]   (■)
     -fix : Performs MD without atom constraints.                      [Default: No]               [-nf](●)
     -nhr : Exec. with no H-bonds. restraints (for production steps).  [Default: No]               [-hr]   (■)
     -clr : Cleaning unnecessary files (after extraction).             [Default: No]               [-cl]   (■)
     -cpt : Compact output files.                                      [Default: No]               [-cp]   (■)
     -ext : Extract output files.                                      [Default: No]               [-ex]   (■)
     -for : Execute in forced mode (suppressing upper to 2 warnings).  [Default: No]       [FORCE] [-lc](●)(■)
  -------------------------------------------------------------------------------------------------
  ⁽*⁾ Configurable options in automated mode. (●) ORCA available. (■) GROMACS available.

2.1.3. Quickstart Examples#

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