Open Source
Molecular Dynamics

In the most common set up of Gibbs Ensemble Monte Carlo (GEMC) simulation, 2 boxes are utilized to represent vapor and liquid phases. In order to equilibrate the system, different types of moves are used:
1) Translations, rotations, and conformational changes
2) Volume exchanges
3) Particle swaps.
The particles are swapped between boxes to equilibrate the chemical potential, volume moves equilibrate pressure, and the rest of the moves within a box are performed to maintain thermal equilibrium. The main advantage of the GEMC simulation is that coexisting phases can be simulated without a physical interface using a unified partition function. Thus, we used GEMC simulations to determined vapor-liquid coexistence curves for a system.

In order to run GEMC certain input files are needed; the two main input files for each box gemc_nvt_box1.inp.zipgemc_nvt_box2.inp.zip, a topology filetopology_atoms_wat.psf.zip for the particular component, and a bias file that contain information of the approximate potential for that component.bias_template.inp.zip. For example, we have provided here the sample files for 64 water molecules.

Starting with the input gemc_nvt_box1.inp file first, we note that the location of the basis set file, as well as the potential file, is declared(in this case these two files are present in the current working directory). &FORCE_EVAL initializes the parameters needed to calculate the energy and forces to describe your system. The Quickstep module is used in order to use of electronic structure methods.

&FORCE_EVAL
  METHOD Quickstep
  &DFT
    BASIS_SET_FILE_NAME GTH_BASIS_SETS 
    POTENTIAL_FILE_NAME POTENTIAL

The SCF section in the code below generates atomic density.

  &MGRID
    CUTOFF 280
  &END MGRID
  &QS
  &END QS
  &SCF
    SCF_GUESS ATOMIC
  &END SCF

One can increase the SCF iterations by including the MAX_SCF function. Also, EPS_SCF declares the expected SCF convergence. Continuing down the code of the input file, the section shown below details which functional we intend on using, in our case BLYP. We also use the DFTD2 dispersion correction. Additionally, the XC_DERIV function specifies about method used to compute derivatives.

  &XC
    &XC_FUNCTIONAL BLYP
    &END XC_FUNCTIONAL
    &VDW_POTENTIAL
      POTENTIAL_TYPE PAIR_POTENTIAL
      &PAIR_POTENTIAL
        R_CUTOFF 40.0
        TYPE DFTD2
        REFERENCE_FUNCTIONAL BLYP
      &END PAIR_POTENTIAL
    &END VDW_POTENTIAL
    &XC_GRID
      XC_DERIV SPLINE2
      XC_SMOOTH_RHO NONE
    &END XC_GRID
  &END XC

The cell and cell ref of the box 1 in angstorms.

  &CELL
    ABC 13.7151207699 13.7151207699 13.7151207699
    &CELL_REF
      ABC 13.7151207699 13.7151207699 13.7151207699
    &END CELL_REF

After the above section of code, there is a listing of coordinates for each atom. After this, the section

  &KIND H
    BASIS_SET TZV2P-GTH
    POTENTIAL GTH-BLYP-q1
  &END KIND

declares the basis set(TZV2P) intended to be used for the simulation. The following code

&GLOBAL
  PROJECT H2O_MC
  RUN_TYPE MC
  PRINT_LEVEL LOW

is intended to described the type of run. Consequently, RUN_TYPE should be set to MC, as this is what we are running.

&MOTION
  &MC
    ENSEMBLE GEMC_NVT
    TEMPERATURE 398.0
    IPRINT 1
    LBIAS yes
    LSTOP yes
    NMOVES 8
    NSWAPMOVES 640
    NSTEP 5
    PRESSURE 1.013
    RESTART no
    BOX2_FILE_NAME GEMC_NVT_box1.inp
    RESTART_FILE_NAME mc_restart_2

The ENSEMBLE GEMC_NVT illustrates the particular type of simulation. It should be noted that the condition LBIAS yes must be true, as we pre sample moves with a classical potential. The LSTOP function determines whether the simulation increment will be in cycles (no), or in steps (yes). The NSTEP feature gives the number of MC cycles in a particular simulation run, and should be adjusted according to the length of the simulation. The line RESTART no should only be set to 'no' for the initial run, then switched to 'yes' after the first simulation run is complete. The line BOX2_FILE_NAME GEMC_NVT_box2.inp gives the file name of the input for Box2 and uses it as a reference such that the two input files are read together. GEMC_NVT_box2.inp has a similar line that references Box 1, for example: BOX2_FILE_NAME GEMC_NVT_box1.inp.

Sample output files for 64 H₂O molecules are provided below. The input file for Box 1 and Box2 has already been explained above. We additionally include a sample output file,output4.out.zip. Information used to calculate the density at the end of the run is towards the end of the file and looks like the following:

|                   BOX 1                      |
------------------------------------------------

********************************************************************************
Average Energy [Hartrees]:                                        -1085.04223205
Average number of molecules:                                         63.00000000
Average Volume [angstroms**3]:                                       2579.876452
--------------------------------------------------------------------------------
Quickstep Moves                           Attempted       Accepted       Percent
                                                  4              1        25.000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Move Data for Molecule Type     1
--------------------------------------------------------------------------------
Conformational Moves                      Attempted       Accepted       Percent
                                                  9              2        22.222
Bond Changes                              Attempted       Accepted       Percent
                                                  5              2        40.000
--------------------------------------------------------------------------------
Angle Changes                             Attempted       Accepted       Percent
                                                  4              0         0.000  
--------------------------------------------------------------------------------
Conformational Moves Rejected BecauseBox Was Empty:     0
-------------------------------------------------------------------------------
Translation Moves                         Attempted       Accepted       Percent
                                                 12              1         8.333 
--------------------------------------------------------------------------------
Rotation Moves                            Attempted       Accepted       Percent
                                                 11              1         9.091  
--------------------------------------------------------------------------------
Biased Move Data
--------------------------------------------------------------------------------
Bond Changes                              Attempted       Accepted       Percent
                                                  5              5       100.000
--------------------------------------------------------------------------------
Angle Changes                             Attempted       Accepted       Percent
                                                  4              4       100.000
--------------------------------------------------------------------------------
Translation Moves                         Attempted       Accepted       Percent
                                                 12              8        66.667
--------------------------------------------------------------------------------
Rotation Moves                            Attempted       Accepted       Percent
                                                 11              5        45.455
--------------------------------------------------------------------------------
********************************************************************************
------------------------------------------------
|                   BOX 2                      |
------------------------------------------------
********************************************************************************
Average Energy [Hartrees]:                                          -17.20378753
Average number of molecules:                                          1.00000000
Average Volume [angstroms**3]:                                       2579.876452

--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Move Data for Molecule Type     1
--------------------------------------------------------------------------------  
Swap Moves into this box                  Attempted       Empty          Percent
                                                  1              0         0.000
                  Growths                 Attempted       Sucessful      Percent
                                                  1              1       100.000
                    Total                 Attempted       Accepted       Percent
                                                  1              0         0.000
-------------------------------------------------------------------------------
Biased Move Data
--------------------------------------------------------------------------------
********************************************************************************

Additionally, other relevant information is included in this file, such as the percentage of accepted moves.