GOMC’s Output Files

Console Output

A variety of useful information relating to instantaneous statistical and thermodynamic data (move trials, acceptance rates, file I/O messages warnings, and other kinds of information) is printed to the STDIO, which, in Linux, will typically be displayed in the terminal. This output can be redirected into a log file in Linux using the > operator.

$ GOMC CPU NVT in.conf > out_isobutane.log &

Statistical and thermodynamic information is provided in console output.

• Energy

  – Intermolecular (LJ)

  – Intramolecular bonded

  – Intramolecular nonbonded

  – Tail corrections

  – Electrostatic real

  – Electrostatic Reciprocal

  – Electrostatic self

  – Electrostatic correction

  – Total electrostatic energy (sum of real, reciprocal, self, and correction)

  – Total Energy (sum of the all energies)

• Pressure

  • Pressure Tensor (\(P_{xx},P_{yy},P_{zz}\))

  • Total pressure

• Statistic

  • Volume

  • Pressure

  • Total molecule number

  • Total Density

  • Surface Tension

  • Mol fraction of each species

  • Mol density of each species

Detailed move, energy, and statistical or thermodynamic information for each simulation box will be printed in three different sections. Each section’s title will start with MTITLE, ETITLE, and STITLE for move, energy, and statistical information, respectively. The instantaneous values for each section will start with MOVE_#, ENER_#, and STAT_# for move, energy, and statistical values, respectively. Where, # is the simulation box number. In addition, if pressure calculation is activated and enabled to print, pressure tensor will be printed in the console output file. This section starts with PRES_# and print the diagonal value of pressure tensor \(P_{xx}\), \(P_{yy}\),and \(P_{zz}\), respectively. The second element after the title of each section is the step number.

In order to extract the desired information from the console file, “grep” and “awk” commands can be used with a proper title section. For example, in order to extract total energy of the system, the following command needs to be executed in terminal:

$ grep "ENER_0" output_console.log | awk '{print $3}'

Here, “output_console.log” is the console output file and “$3” represents the second element of the “ENERGY_BOX_0” section.

The first section of this console output typically includes some information relating the system, CPU, GPU, and RAM. In continue, console output includes information regarding the input file (configuration file), force field reading, summary of the structure of the molecule, bonded and non-bonded parameters, and minimum and maximum coordinate of molecules. This output is important; it may contain text relating to issues encountered if there was an error in the current run (e.g. a bad parameter, unknown keyword, missing parameters in the configuration file, etc.)

Printing summary of configuration file.

Reading parameter file and printing the summary of the force field.

Reading the PDB files for each box, printing the min and max coordinates.

Next, the energy and statistic title, initial energy and statistic of the system’s starting configuration will print:

#################################
# ENABLE:         BLK, FLUC.
#################################
OutEnergy         true  true
OutPressure       true  true
OutMolNum         true  true
OutDensity        true  true
OutVolume         true  true
OutSurfaceTension false false

Printing initial energy of the system and statistical values.

After the simulation starts, move, energy, and statistical title, followed by their values for each simulation box, will print:

At the end of the run, Monte Carlo move acceptance for each molecule kind and simulation box, total amount of time spent on each Monte Carlo move, total timing information, and other wrap up info will be printed.

Block Output Files

GOMC tracks a number of thermodynamic variables of interest during the simulation and prints them all in one file for each box.

• Energy

  – Intermolecular (LJ)

  – Intramolecular bonded

  – Intramolecular nonbonded

  – Tail corrections

  – Electrostatic real

  – Electrostatic Reciprocal

  – Total Energy (sum of the all energies)

• Virial

• Statistic

  • Pressure

  • Surface Tension (using virial method)

  • Volume

  • Total molecule number

  • Total Density

  • Mol fraction of each species

  • Mol density of each species

  • Heat of vaporization

Printing the average energy of the system and statistical values.

At the beginning of each file, the title of each property followed by their average values is printed. Desired data can be extracted, as explained before, using the “awk” command. For example, in order to extract total density of the system, the following command need to be executed in terminal:

$ cat Blk_OutputName_BOX_0.dat | awk '{print $2}'

Here, “Blk_OutputName_BOX_0.dat” is the block-average file for simulation box 0 and “$2” represents the second column of the block file.

#################################
# ENABLE:         BLK, FLUC.
#################################
OutEnergy         true  true
OutPressure       true  true
OutMolNum         true  true
OutDensity        true  true
OutVolume         true  true
OutSurfaceTension false false

PDB Output Files

GOMC capables of outputing the molecular coordinates during the simulation in PDB format. GOMC outputs two type of PDB files:

1. The last state of simulation at a specified step (OutputName_BOX_n.pdb, where n defines the box number).

2. The state of simulation at a specified step (OutputName_BOX_n_restart.pdb, where n defines the box number).

1. Restart Trajectory

The restart PDB file contains only ATOM that exist in each boxes at specified steps. This allows the user to load this file into GOMC once Restart simulation was active. If restart PDB output was enabled, one file for NVT or NPT and two files for Gibbs ensemble or grand canonical ensemble will be outputed. Header part of this file contains important information and will be needed to restart the simulation:

• Simulation cell dimensions and angles.

• Maximum amount of displacement (Å), rotation (\(\delta\)), and volume (\(\AA^3\)) that used in Displacement, Rotation, and Volume move.

The coordinates of isobutane molecules in simulation Box 0, at steps 30000, in OutputName_BOX_0_restart.pdb file.

The coordinates of isobutane molecules in simulation Box 1, at steps 30000, in OutputName_BOX_1_restart.pdb file.

Note

The frequency of printing restart PDB file is controlled by RestartFreq parameter in configuration file.

Important

The beta value in restart PDB file defines the mobility of the molecule.

• Beta = 0.00: molecule can move and transfer within and between boxes.

• Beta = 1.00: molecule is fixed in its position.

• Beta = 2.00: molecule can move within the box but cannot be transferred between boxes.

2. Simulation Trajectories

The trajectory PDB file contains an entry for every ATOM, in all boxes read. This allows VMD (which requires a constant number of atoms) to properly parse the simulation frames. If PDB output was enabled, one file for NVT or NPT and two files for Gibbs ensemble or grand canonical ensemble will be outputed. Header part of this file contains simulation cell dimensions and angles, frame number, and simulation steps.

The coordinates of all isobutane molecules at beginning of the simulation, in OutputName_BOX_0.pdb file.

The coordinates of all isobutane molecules at beginning of the simulation, in OutputName_BOX_1.pdb file.

Note

The frequency of printing trajectory PDB file is controlled by CoordinatesFreq parameter in configuration file.

Important

• For atoms not currently in a box, the coordinates are set to < 0.00, 0.00, 0.00 >.

• The occupancy value defines the box, which molecule is in (box 0 occupancy=0.00 ; box 1 occupancy=1.00)

• The beta value in trajectory PDB file defines the mobility of the molecule.

  • Beta = 0.00: molecule can move and transfer within and between boxes.

  • Beta = 1.00: molecule is fixed in its position.

  • Beta = 2.00: molecule can move within the box but cannot be transferred between boxes.

PSF Output File

Molecule Distribution Output File

In grand canonical Monte Carlo (GCMC) simulation, GOMC outputs a binned number of molecules, observed in the system. This file can be used to detect the overlap between various GCMC simulation states. Sufficient overlap between various GCMC simulation is required in histogram reweighting method.

The molecule distribution will be outputed to a file, with a name constructed from parameters defined in configuration file (DistName, RunNumber, and RunLetter). For instance, for the first molecule kind and following parameters in configuration file

#################################
# OutHistSettings
#################################
DistName   dis
RunNumber  3
RunLetter  a

GOMC will output the molecule distribution into “n1dis3a.dat” file.

Molecule number distribution taken for isobutane simulation in GCMC simulation. The field in molecule distribution file, from left to right are number of molecule observed in the simulation and number of samples.

Histogram Output File

In grand canonical Monte Carlo (GCMC) simulation, GOMC outputs the observed number of molecule (for each molecule kind) and energy of the system (nonbonded + LRC). This file only will be used for histogram reweighting purposes.

The histogram will be outputed to a file, with a name constructed from parameters defined in configuration file (HistName, RunNumber, and RunLetter). For instance, for the following parameters in configuration file

#################################
# OutHistSettings
#################################
HistName   his
RunNumber  3
RunLetter  a

GOMC will output the histogram data into “his3a.dat” file.

The header of the histogram file contains information of the simulated system, such as temperature, number of molecule kind, chemical potential, and x, y, z dimensions of simulation box.

The histogram taken for isobutane simulation in GCMC simulation. The field in histogram file, from left to right are number of molecule observed for the first molecule kind in the simulation and energy of the system (nonbonded + LRC).

Free Energy Output File

GOMC is capable of calculating absolute solvation free energy in NVT and NPT ensemble, using thermodynamic integration and free energy purturbation methods. GOMC outputs the raw informations, such as the derivative of energy with respective to current lambda (\(\frac{dE}{d\lambda}\)) and energy different between current lambda state and all other neighboring lambda states (\(\Delta E_{{\lambda}_i \rightarrow {\lambda}_j}\)), which is essential to calculate solvation free energy with various estimators, such as TI, BAR, MBAR, and more.

The header of Free_Energy_BOX_0_ OutputName.dat contains the following information:

• Temperature of the simulation.

• The index of the lambda vector.

• Value of \({\lambda}_{Coulomb}\) and \({\lambda}_{VDW}\).

• Monte Carlo step number.

• Total energy of the system.

• Derivative of energy with respective to lambda for coulomb interaction (\(\frac{dE}{d\lambda_{Coulomb}}\)).

• Derivative of energy with respective to lambda for VDW interaction (\(\frac{dE}{d\lambda_{VDW}}\)).

• Energy different between current lambda state and all other neighboring lambda states (\(\Delta E_{{\lambda}_i \rightarrow {\lambda}_j} = E_{{\lambda}_j} - E_{{\lambda}_i}\))

Snapshot of GOMC free energy output file (Free_Energy_BOX_0_ OutputName.dat).

Checkpoint Output File

GOMC has the ability to save the state to a file and continue as if no interruption occurred through the use of Checkpoint files. The checkpoint file is not human-readable.