Molecular dynamics module

Simulation of water

 

Objective: to create a model of water and study the calculation of thermodynamic properties from a molecular dynamics simulation using DISCOVER

 

Criteria for analysis:

    1. Heat of vaporization (U) of the liquid.
    2. Consistent density and pressure.
    3. Radial distribution function.
    4. Dipole-dipole correlation function
    5. Self-diffusion coefficient
    1. velocity autocorrelation function
    2. mean-square displacement.

 

Method: create a box of water molecules using the BUILDER module of INSIGHT. This box of water molecules has already been minimized and is ready for action. Note the difference between this starting point and the face-centered cubic lattice that we used for argon. In the case of argon we had to minimize then thermally equilibrate to the collection of atoms to create a realistic model of the liquid. Since this has already been done for you with the water box you can immediately begin modeling the thermodynamics and structure of liquid water. The INSIGHT program allows you to create a solvent box and to "soak" a solute molecule using the particular solvent box. Note that you must have a solvent molecule in order to use the soak command to create a solvent box. The solvent may be an ion, small molecule or a protein or DNA molecule. In the present example we will use water itself as the "solute". This is because we wish to form a box that contains only water in order to study the properties of liquid water.

 

Go to the Builder pull-down menu. Use the Fragment/Get command and select hydroxy from the FRAGMENT_WINDOW to create the water molecule. The FRAGMENT_WINDOW will contain a number of groups. These groups can be used individually or can be bonded together. Once a water molecule has appeared on the screen the menu will be altered to allow you select a second fragment. For this module just select Cancel to exit the Fragment pull-down menu. Now you should see a single water molecule in the center of the monitor. The single water molecule you have created will serve to nucleate the solvent box.

 

Use the Assembly/Cell command on the INSIGHT (upper) menu bar to create a solvent box. The menu choices you should select are

Lengths

a 18.62

b 18.62

c 18.62

Angles

a 90.00

b 90.00

c 90.00

Click on the center in cell box (it should turn yellow). When you select execute the water molecule will move up and you will see the outline of the solvent box you have created. Select Cancel and the active menu will disappear.

Then select Assembly/Soak

Method: Select PBC for Periodic Boundary Conditions.

Once selected the diamond should turn yellow indicating the selection. You will note that the Solvent File is $INSIGHT_DATA/water_box.psv.

Select Execute.

You will see blue water molecules fill the solvent box.

Now return to the Assembly menu and select Assembly/Associate. The two objects you will need to associate are the central water molecule you have used as a seed for the soak command and the 217 water molecules that have filled the box. You can name the assembly water or some other appropriate name.i

To assign parameters to the water molecules use the FF button on the left of the INSIGHT display. Select Fix for both Potential Action and Partial Chg Action. You can leave Formal Chr Action as accept since we have no formal charges.

You can either save this file or continue using it to run DISCOVER.

To save the file use the Molecule/Put command and give the file a name of your choosing. If you want to read in the molecule again use the Molecule/Get command.

If you examine the *.car file you should find the coordinates for 218 water molecules. The *.mdf file should include atom types and charges. Make sure that the charges and atom types are consistent between your "solute" water (this will be the first one in the list) and the remaining 217 solvent waters. The charges should be

O = -0.82

H = 0.41

Of course, since there are two Hs for each O the charges add to zero.

 

The water box is the starting point for molecular dynamics simulations in three stages

  1. energy minimization.
  2. equilibration.
  3. constant volume or constant pressure dynamics.

 

Use the DISCOVER3 pulldown menu to create a second menu bar below the INSIGHT menu bar. In DISCOVER3 choose the system for study using the Setup/System menu. Under Disco Object Name you should see WATER_ASSY (or the corresponding assembly name that you gave the object). The parameter box should be set to assembly to read in both the "solute" water (usually this is OBJECT 1) and the solvent water (usually this is OBJECT 2). Make sure that the box is checked (yellow) for PBC On. This turns on periodic boundary conditions in the calculation.

Select Execute.

The Specify/Nonbonds command allows you to specify the cut-off or other treatment of long range interactions. In the Nonbonds menu select the following

PBC Sum Method [Group_based]

Cutoff Distance [9.0]

Spline width [1.0]

Buffer width [0.5] (this determines how far any atom must move before the neighbor list is updated).

Select Execute.

 

To set up the energy minimization stage use the Calculate pull-down menu. Under Calculate/Minimize select the following

Max Steps [10000]

Final Convergence [0.001]

Select execute.

 

To set up the stages of dynamics use the Calculate pull-down menu. Under Calculate/Dynamics select the following

Run Time fs [5000.0]

Velocity [Create] (check the box to turn it yellow)

PBC Ensemble [NVT_PBC] (check the box to turn it yellow)

Temperature [desired temperature]

Select execute.

 

Note: these instructions assume that you want to run a constant number, volume, and temperature, or NVT ensemble. Note that this is the canonical ensemble. If instead you wish to run with a constant number, pressure, and temperature or NPT ensemble you will need to select NPT above instead of NVT. Note that the NPT ensemble is the isobaric-isothermal ensemble.

 

To set up the stages of dynamics use the Calculate pull-down menu. Under Calculate/Dynamics select the following

Run Time fs [20000.0]

Velocity [Current] (check the box to turn it yellow)

PBC Ensemble [NVT_PBC] (check the box to turn it yellow)

Temperature [desired temperature]

Select execute.

 

To write a history file (e.g. water_1.his) that will be used in the data analysis use the Analyze/Output command to generate a menu. Choose the second dynamics stage for analysis (this should be 5 dynamics if you have followed everything exactly up to this point).

 

File type [history] (check the diamond to turn it yellow)

To instruct the INSIGHT program to write an input file that you can modify and run in background mode on the computer go to the Background_Job/Setup_Bkgd_Job menu.

Submission mode [immediate]

Execution mode [cmd_file_only]

Box for

Host [local]

Select Execute

Use the D_run/Run command to write the background file.

 

Once you have written the file, you will want to examine it.

You will need to use "more" or the "vi" editor.

 

Look at the water_1.car file to see a list of the atomic coordinates and the dimensions of the box for periodic boundary conditions. You will also want to check that PBC=ON in this file, meaning that periodic boundary conditions have been activated. Check to be sure that the charges have been set correctly on the first water molecule. The first molecule is the seed that you used to generate the box and the surrounding solvent.

 

In another window run the job using

To examine the progress of the job observe the *.pek file