Molecular dynamics module

Analysis of argon simulation

Once the job is complete you can analyze the results using the DECIPHER module.

You will find the following files in the directory where you ran the job:

[jobname].car is the initial Cartesian coordinate file.

[jobname].cor is the final frame or time point after dynamics.

[jobname].mdf is the molecular data file.

[jobname].inp is the input file. This file contains the cutoffs and stages for the simulation including control variables.

[jobname].out is the output file. This file contains information on the CPU usage and average properties as well as a record of the force field used etc.

[jobname].his is the history file. This file contains the trajectory of your run including all of the positions and velocities of the particles.


First you will want to examine the output file to make sure that your run was successful.

Note: The Background [on] flag below is not absolutely necessary. It tells the DECIPHER module to generate a file so that you can submit a job in background mode. By this we mean that the job is submitted to a processor and you can continue to use INSIGHT or DECIPHER in the foreground. If you do not use this flag then your screen will be blank and not usable during the 1-30 minutes required for the job. This is a good time to read McQuarrie.

Note2: The file names and Create_TBL_File end in .tbl as a default. You will have to rename them later. For example, if the radial distribution function enu creates rahman_864)rdf.tbl by default, then you can rename it later. You type >cp rahman_864_rdf.tbl [newname].rdf where [newname] is the name indicated in the section on file handling at the bottom of this page.

Read in the rahman_864.cor file using the Molecule/Get command in INSIGHT. After running dynamics you will see an apparently unstructured argon solvent as shown below.

Use the side pull-down menu to run DECIPHER. In decipher use the Configurations/Get command to generate a menu. Use the Files list on the right-hand side to get the rahman_864.his file.

Configurations File [rahman_864.his]

Assembly/molecule [RAHMAN_864]

Load_Cell (check the box to turn it yellow)

Load_Pressure (do not check the box)

Load_Velocities (check the box to turn it yellow)

Frame Spec [*] (reads all of the frames)

Select execute.

Radial Distribution Functions

To calculate the radial distribution function averaged over the entire trajectory (i.e. averaging all of the frames in the history file) use the

Spectra/RadialDistFunc command.

Distribution_type [pair]

Molecule_Spec [RAHMAN_864]

Molecule_2_Spec [same]

Coord_Number [on] (check the box to turn it yellow)

Bulk_Density [on] (check the box to turn it yellow)

Data_Sources [trajectory] (check the box to turn it yellow)

Background [on] (check the box to turn it yellow)

Create_TBL_File [rdf] (check the box to turn it yellow)

Mean Square Displacement

To calculate the mean squared displacement use the Spectra/Mean_Sq_Disp command.

Molecule_Spec [RAHMAN_864]

Data_Source [trajectory]

Frame_Spec [*]

Output

MSD [on] (check the box to turn it yellow)

Dist_Traveled [on] (check the box to turn it yellow)

Background [on] (check the box to turn it yellow)

Create_TBL_File [msd] (check the box to turn it yellow)

Velocity Autocorrelation Function

To calculate the velocity correlation function and associated spectral density first use the Functions/Velocity menu.

Function/Name [velocity1]

Definition levels

Per_Atom [on] (check the diamond to turn it yellow)

Molecule_Spec [RAHMAN_864]

Then use the Spectra/TimeCorrFunc pulldown

Function Spec [velocity 1] (you can find this under Parameters/Function Levels Vector on the right side or you can simply type it in).

Function 2 Spec [same]

Output

Corr_Func [on] (check the box to turn it yellow)

Spectral_Density [on] (check the box to turn it yellow)

Zero padding [on] (check the box to turn it yellow)

Calculation method

Direct [on] (check the box to turn it yellow)

t0_step [1]

t_length [200]

Frame Spec [*]

Background [on] (check the box to turn it yellow)

Create_TBL_File [vacf] (check the box to turn it yellow)