1. Executing CHARMm Dynamics

This chapter describes CHARMm dynamics calculations and the Dynamics Animation application that is used for viewing and analyzing CHARMm dynamics trajectories.

CHARMm dynamics simulates the natural motion of a molecular system and produces a set of coordinates and velocities that describes the atomic motions of the system over time. The resulting dynamics trajectory can be viewed in the Dynamics Animation application and analyzed in the Analysis application. A typical molecular dynamics run involves heating, equilibration, and simulation

All dynamics calculations begin with an initial set of Cartesian coordinates that are derived from experimental data or selected parameters. (See citation 1 under References). The energy of a molecular structure is minimized to remove bad contacts and to relax strained torsion angles before a dynamics simulation is started. It is not necessary to minimize to an absolute minimum, since the conformation of the structure changes during heating. Structures that do contain bad contacts between atoms or highly strained torsion angles can cause abnormally large forces on some atoms and unrealistic simulation results.

With the Dynamics Animation application, you can interactively display a dynamics trajectory calculated by CHARMm, CNX, or X-PLOR. Displays can include a graphical representation of hydrogen bonding, interatomic distances, atomic positions, molecule energy, or other atomic properties.

The dynamics trajectory calculated in CHARMm consists of datasets of atom coordinates written at periodic intervals. If the trajectory is thought of as a movie, then each individual dataset may be considered a frame. You can display the trajectory frame-by-frame at any desired speed. Single frames may be saved to individual MSFs that can be compared in detail using the Molecular Similarity application.

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Commands in the CHARMm pulldown

Table 1. CHARMm Menu in QUANTA

Command	Sub Option	Function
Select CHARMm Host		Allows the user to specify the host machine to execute a CHARMm job and point to the appropriate executable
CHARMm Initialization Options		Set up initialization options for CHARMm
	Bomb Level	Specify checking level for termination errors
	Warning level	Specify checking level for warnings
	Print Level	Specify level for verbosity
	CHARMm log destination	Location of output
	CHARMm Stream file for additional initialization commands	Location of CHARMm script with miscellaneous, user-defined initialization options.
CHARMm Process		Specify CHARMm initialization options
pullright	Initialize interactive	Initialize interactive QUANTA/CHARMm communication
pullright	Terminate interactive	Terminate interactive QUANTA/CHARMm communication
pullright	Interactive status	Show status of interactive QUANTA/CHARMm communication
Energy Terms		Specify which energy terms will be used
Update Parameters		Specify update parameters Frequency of updates Cutoff distances Smoothing function Dielectric model Image update parameters Ewald summation options
Minimization options		Options for CHARMm minimization
Dynamics options		Options for CHARMm dynamics
	Setup Heating	Options for heating
	Setup Equilibration	Options for equilibration
	Setup Simulation	Options for production simulations
	Setup Detailed Dynamics	Detailed options for MD simulation
Constraint Options
pullright	Set Atom Constraints	Create/setup CHARMm constraints
pullright	Atom Constraints On	Turn on constraints
pullright	Atom Constraints Off	Turn off constraints
pullright	Dihedral/Distance	Create/setup dihedral and distance constraints see Applying Constraints
pullright	Dihedral on	Turn on constraints
pullright	Dihedral off	Turn off constraints
pullright	Distance on	Turn on constraints
pullright	Distance off	Turn off constraints
Shake Options		Setup SHAKE options
Parameters		CHARMm parameter options
pullright	Read Parameters	Location of *.prm file
pullright	Save Parameters	Location to save custom parameter file
pullright	Set Options	Parameter options
CHARMm Mode		Set CHARMm operation mode
pullright	PSF	PSF mode
pullright	RTF	RTF Mode
pullright	MMFF	MMFF mode
pullright	MMFFS	MMFFS mode
pullright	PSF Terms	Select PSF terms
pullright	RTF options	RTF settings
Get Fourth parameter		Setup forces and scalar parameters
pullright	Forces	Force options
pullright	Scalars	Scalar options
Optimize hydrogens		Optimize hydrogens using CHARMm hbuild
Solvate structure
pullright	15A Radius Sphere	Solvate molecule in sphere of radius 15 A
pullright	15A Length Box	Solvate molecule in periodic box of waters with edge length 15A
pullright	30A Length Box	Solvate molecule in periodic box of waters with edge length 30A
pullright	Solvate residues 8A	Solvate residues to 8A
pullright	Solvate residues 10A	Solvate residues to 10A
pullright	15A methanol sphere	Solvate in a sphere of methanol with radius 15A
pullright	Water image 15A	Turn on 15A water image file
pullright	Water image 30A	Turn on 30A water image file
pullright	Turn of Water image	Turn of image options
Periodic boundaries		Setup periodic boundary conditions
Send CHARMm command		Console for entering CHARMm commands
Stream CHARMm file		Location of CHARMm standalone stream file
Capture CHARMm commands		Options to turn on/off capture of CHARMm commands
pullright	On	Select file to capture CHARMm commands
pullright	Off	Turn off capturing
pullright	Suspend	Suspend capture of CHARMm commands
pullright	Restart	Restart capture of CHARMm commands
Settings		Options for capturing settings
pullright	Show	Examine various setup options
pullright	Save	Save CHARMm setup file to specified location
pullright	Restore	Read CHARMm setup file from specified location

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Running CHARMm dynamics calculations

A typical molecular dynamics run involves heating, equilibration, and simulation. Parameters are set for each stage in a run. Table 2 lists parameter categories and provides a brief description of each. Structures must be minimized before they are used in dynamics runs.

Table 2 . CHARMm Dynamics Setup dialog box 

Option	Description
Dynamics Steps	Determines the total number of steps of dynamics to calculate for this stage of basic dynamics. The number of steps that may be specified for equilibration and simulation depends on the nature of the study. The heating stage requires that the number of steps be large enough to allow a reasonably smooth increase in temperature in the molecular system.
Restart Read File   Restart Write File	Specifies filenames used for restarting dynamics calculations. Restart files store the final velocities and coordinates of a molecular structure at the end of a stage of dynamics. The Restart Write File of one stage is typically the Restart Read File of the next. Restart files are automatically given a .RST extension.
Coordinate Trajectory File	Specifies the name of the file to which the dynamics trajectory is written at the end of this stage of the calculation. The number of sets of coordinates in this file is the number of steps of dynamics divided by the output frequency. Trajectory files are automatically given a .DCD extension.
Energy Values File	Contains the energy values corresponding to each set of coordinates saved in the coordinate trajectory file. The saved energy information includes time step, total energy, potential energy, kinetic energy, and temperature. Energy value files are automatically given a .ENE extension.
Output Frequency	Specifies, in steps, the frequency with which coordinates and energies are saved to the coordinate trajectory and energy files.
Time Step	Specifies the integration time step for the dynamics calculation. The time step must be sufficiently small to maintain energy conservation and trajectory accuracy. A large time step reduces the total time required to calculate a trajectory.
Initial Temperature   Final Temperature	Specifies the temperatures at the beginning and end of dynamics heating. In a typical dynamics study, a molecular system is slowly heated from absolute zero (0 K) to room temperature (300 K) to raise the kinetic energy with minimal conformational changes. It is then equilibrated for a time at 300 K to stabilize the temperature. These two steps are typically performed once. Thereafter, multiple simulation stages may be run to show conformational changes over time. If the heating and equilibration stages are omitted, the dynamics simulation may be run directly at the desired temperature. In this case, the initial and final temperatures are given the same values.
Start ... from the beginning	Specifies that the calculation is to start without a predetermined set of energies. If all three stages of basic dynamics are to be run, this option is selected in the heating setup dialog box only. If heating and equilibration are not to be run, this option is selected in the simulation setup dialog box.
Restart... from the Restart File	Specifies that the calculation is to start using initial velocities and coordinates stored in the Restart Read File. If all three stages of dynamics are to be run, this option is selected in the equilibration setup and simulation setup dialog boxes. The restart from Restart File option is rarely selected in the heating setup dialog box.
Do Not Run	Specifies that this stage of dynamics is not to be run.

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Heating

A minimized structure represents a molecule at a temperature close to absolute zero (0 K). Molecular dynamics simulations are usually run at room temperature (300 K). Kinetic energy is slowly and uniformly added to the system over time intervals by randomly assigning velocities to each atom to achieve the final temperature.

Dynamics heating occurs over several picoseconds, depending on the size of the molecular system. The recommended heating rate is 0.1 K per step. Small systems can be heated at a faster rate. Some large systems may require heating at a slower rate.

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Equilibration

When the structure reaches the temperature at which the dynamics trajectory is to be computed, it must be equilibrated. Dynamics equilibration is achieved by allowing the molecular system to evolve spontaneously for a period of time, integrating the equations of motion until the average temperature and structure remains stable. Equilibration is facilitated by periodically scaling velocities appropriately for the desired temperature. The procedure is continued until the statistical properties of the system become independent of time.

The equilibration temperature must correspond to the final temperature used in heating. If you want an equilibration temperature different from the final heating temperature of the heating phase, the heating step must be repeated.

The Restart Write File generated during heating is used as the Restart Read File for the equilibration phase. Although a separate trajectory file is created, the equilibration trajectory is a continuation of the heating trajectory.

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Simulation

The final step of a dynamics run is dynamics simulation. Simulation takes an equilibrated structure as its starting point and produces a dynamics trajectory. In a typical simulation, the trajectory traces the motions of the macromolecule for a specified time.

Dynamics heating and equilibration are usually performed only once on a molecular structure. Simulation can be run several times to show changes in the conformation of the molecule over time.

The simulation temperature must correspond to the equilibration temperature. The Restart Write File generated during equilibration is used as the Restart Read File for simulation. Although a separate trajectory file is created, the equilibration trajectory is a continuation of the heating and equilibration trajectories.

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Saving dynamics output

At the completion of dynamics simulation, the final frame of the calculated trajectory is displayed in the viewing area. The final frame's energy is displayed in the upper right corner. In the Modeling palette, Undo Changes, Save Changes, and Reject Changes become active because the displayed conformation is different from the starting conformation. One of these tools must be selected before further modeling can be carried out on the displayed structure.

In most cases, select Reject Changes from the Modeling palette to restore the last saved set of coordinates for the structure. Otherwise, initial coordinates are not saved, since these coordinates are not part of the trajectory.

All coordinates calculated during a dynamics run are stored in the coordinate trajectory file specified in the dynamics setup. Each set of coordinates in the dynamics trajectory can be viewed using the Dynamics Animation application. You also can read data into an individual MSF. The final set of coordinates is stored in CHARMm external format at the end of the calculation. Table 3 lists file types and describes each briefly.

Table 3. Dynamics output files 

File Type	Description
Dynamics Trajectory File (.DCD)	Contains all the coordinate sets defining the dynamics trajectory for the calculated stage of dynamics, in CHARMm binary format. May be viewed in the Dynamics Animation application or analyzed in the Analysis application.
Energy File (.ENE)	Contains energies stored periodically throughout the dynamics calculation, in ASCII format. May be viewed using Plots or Graphs from the File menu.
Restart File (.RST)	Contains final velocities and coordinates and can be used as a starting file for additional dynamics calculations. ASCII format.
Velocity Trajectory File (.DVL)	Contains velocities at intervals throughout the dynamics calculation. Available only from detailed dynamics. Binary format.
Coordinate File (.CRD)	Contains the final coordinates at the end of the calculation of a particular stage of dynamics. Stored in CHARMm coordinate format (ASCII).
CHARMm Log File	Contains input and output from modeling the structure in CHARMm and running the dynamics calculation. Contains energy and dynamics-related summaries written periodically throughout the calculation. ASCII format. The actual filename, including extension, is specified in the charmm.cis file; default is CHARMm.LOG.

Complete the following exercise to become familiar with the procedures for executing a dynamics run. This exercise uses mypeptide.msf, which is generated in Chapter 4 of QUANTA Generating and Displaying Molecules. Complete Chapter 4 before proceeding.

1.   Open an MSF

Display the File menu. Select Open. A File Librarian dialog box opens. Select mypeptide.msf from the scrolling list. Select the Open button. The structure is displayed in the viewing area.

Make sure the Shake option is on. Display the CHARMm menu. Select Shake Options. Accept the default settings:

Run dynamics with Shake ON.
Shake Tolerance: 1e-09
Maximum number of iterations: 500
Use Parameter-specified Geometry

Select the OK button.

2.   Select heating parameters and heat the structure.

Display the CHARMm menu. Select the Dynamics option. The CHARMm Dynamics Setup dialog box is displayed offering options for the selection of heating, equilibration, and simulation conditions.

Select Setup Heating.

Select the OK button. A dialog box is displayed offering the ability to change heating conditions from their default values. Enter the values:

Dynamics Steps: 600
Restart Write File: mypep_h
Coordinate Trajectory File: mypep_h
Energy Values File: mypep_h
Output Frequency: 10
Time Step: 0.00100
Initial Temperature: 0.00
Final Temperature: 300.00

Selecting these parameters produces a heating trajectory of 0.6 ps (600 steps x 0.001 ps/step). Every tenth step is saved into a trajectory file that is 60 frames long.

Also select the option Start Heating From The Beginning.

Select the OK button. The specifications are defined and the CHARMm Dynamics Setup dialog box is redisplayed.

3.   Select equilibration parameters and equilibrate the structure.

From the CHARMm Dynamics Setup dialog box, select the option:

Setup Equilibration

Select the OK button. A dialog box is displayed offering the ability to adjust the equilibration specifications.

Enter the values:

Dynamics Steps: 600
Restart Read File: mypep_h
Restart Write File: mypep_e
Coordinate Trajectory File: mypep_e
Energy Values File: mypep_e
Output Frequency: 10
Equilibration Frequency: 10
Time Step: 0.00100
Temperature: 300.00

Then select:

Restart Equilibration From The Restart File

Select the OK button. The specifications are defined and the Dynamics Options dialog box is redisplayed.

4.   Select the simulation parameters.

From the CHARMm Dynamics Simulations Setup dialog box, select the option:

Setup Simulation

Select the OK button. A dialog box is displayed, offering the ability to adjust the simulation specifications.

Enter the values:

Dynamics Steps: 600
Restart Read File: mypep_e
Restart Write File: mypep_s
Coordinate Trajectory File: mypep_s
Energy Values File: mypep_s
Output Frequency: 10
Time Step: 0.00100
Temperature: 300.00

Select the option:

Restart Simulation From The Restart File

Select the OK button. The specifications are defined and the dialog box containing the dynamics options is redisplayed.

Select the DONE button. The dialog box is cleared from the screen.

5.   Execute the dynamics calculation.

Display the Modeling palette. Select CHARMm Dynamics. The selection is checked and highlighted.

CHARMm automatically starts the dynamics calculation, using the defined specifications. Status information is printed in the message line, indicating the progress of the CHARMm calculation. The calculation can take 10 min or more.

Each frame of the dynamics trajectory and the energy for that conformation are displayed in the viewing area as the calculation proceeds. The time and temperature of the simulation are also displayed in the message line.

The results of the dynamics calculation are automatically stored in the output files specified in the dynamics setup.

6.   Do not save the results of the calculation to an MSF.

From the Modeling palette, select Reject Changes. The structure using the last saved set of coordinates for mypeptide.msf is displayed in the viewing area.

7.   Display hydrogen bonds for mypeptide.msf.

From the Modeling palette, select Hydrogen Bonds. Bonds are displayed as white dashed lines. They also are displayed when the dynamics trajectory is animated.

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Executing dynamics animation

The procedure for displaying a dynamics trajectory in the Dynamics Animation application involves four steps:

1.   Assemble a list of coordinate trajectory files that make up the trajectory.

2.   Specify datasets from the collection of trajectories files to be displayed and the information to be graphically represented in the display.

3.   Download the selected set of datasets into memory for display as frames to create the animation.

4.   Interactively display the selected set of frames.

When Dynamics Animation is selected from the Application menu, the Dynamics Animation palette is displayed over the Modeling palette. In addition, a Dynamics dial emulator is displayed in the Dial Emulator window. Table 4 lists the selections in the palette and provides a brief description of each. The table also provides a description of the dynamics dial.

Table 4. Dynamics Animation palette and dials 

Selection	Description
Select Trajectories	Assembles the list of coordinate trajectory files from which the dynamics frames to be downloaded are specified.
Set Up Animation	Specifies the frames that are to be downloaded and the graphic items or display features that are to be generated for downloaded frames. Also sets the rate of animation display.
Color By Velocity	Allows a velocity file to be specified; the animation is then created using these velocities to color each atom in each frame. The colors range from white (slowest) to red (fastest).
List Settings	Lists the setup specifications in the textport.
Create Animation	Downloads dynamics frames into memory as specified by Set Up Animation.
Open Energy File	Selects a new energy file for display in the energy trace.
Display Energy Trace	Toggles on and off the display of the energy trace.
Clock	Continuously displays dynamics frames in one direction.
Cycle	Continuously displays dynamics frames in both directions alternately.
Select Frame	Specifies a new atom reference frame.
Fix Atom Position	For all dynamics frames, fixes the atom that you select as the display origin.
Release Atom	Returns the display origin for all dynamics frames to the center of the structure.
Delete Dynamics Frames	Deletes dynamics frames from memory.
Write Frame to MSF	Writes the coordinates of a dynamics frame to an MSF.
Exit Dynamics Animation	Exits Dynamics Animation and returns control to Molecular Modeling.
Dynamics Dial	Horizontal dial scans frame-by-frame through the trajectory.
Speed Dial	Vertical dial controls the frame display rate of the continuous display selections (Clock and Cycle).

A list of one or more coordinate trajectory files must be defined before a dynamics animation can be displayed. A single trajectory is assembled using Select Trajectories on the Dynamics Animation palette. Table 5 lists and describes the options in the dialog box that is displayed when Select Trajectories is selected.

Table 5. Select Trajectories Options

Option	Description
Initialize Dynamics Files	Displays the File Librarian with a list of available dynamics files. By selecting a dynamics file from the File Librarian, you initialize a new list with the chosen file as the first entry. The first file in the list is used to set appropriate default values for the first and last animation frame and the step size between animation frames.
Change a File	Displays a scrolling list dialog box showing the current files in the list. Select the file to be replaced, then the File Librarian lists dynamics files in your current directory. Selection of a coordinate trajectory file from the File Librarian causes that file to replace the previously selected file in the list.
Add a File	Displays a File Librarian listing available dynamics files. Selecting a file adds that file to the end of the current list. Dynamics files must be added to the list in the order in which they are to be displayed.
Delete a File	Displays a File Librarian showing the current files in the list. Selecting one of these files causes that file to be removed from the list. Subsequent files in the list are renumbered.
List Current Files	Displays names of currently used coordinate trajectory files in the textport. The files are numbered sequentially in the order in which they are to be displayed.
Show File Headers	Displays the header block of the specified coordinate trajectory files in the textport.
Binary or Hexadecimal Files	Specifies whether the trajectory to be loaded was written in binary or hexadecimal format. The latter format is useful when producing trajectories on a remote compute server for display on the graphics workstation.

Multiple files from the trajectories list are combined into a single animation. The composite trajectory from the datasets in these files also is specified for graphic display and analysis.

The file header in each coordinate trajectory file contains critical information including:

• The number of datasets in the file.

• The starting dataset of the file.

• The number of time steps between successive datasets in a dynamics trajectory.

This information is required to specify the range of datasets to be viewed. The application automatically uses the dataset information contained in the first trajectory file. It does not automatically combine dataset information contained in a series of trajectory files. The trajectory files must be reviewed to determine:

• The Dataset Range From value - the starting dataset value in the header of the first trajectory.

• The Dataset Range To value - the ending dataset value in the header of the last trajectory.

• The Step Size value in the header of each trajectory

Additional information that may be graphically represented in the animation includes:

• Atom labels

• Distances

• Hydrogen bonds

Specifications for this information are established using Set Up Animation in the Dynamics Animation palette. Each frame of the dynamics trajectory is loaded into memory before an animation is displayed. Set Up Animation governs the creation process. Table 6 lists options in the Set Up Animation dialog box and provides a brief description of each.

Table 6. Set Up Animation dialog box 

Option	Description
Use CHARMm Header	Retains the dataset numbers contained in the dynamics file headers. This is the default. It can be used for animations composed of a single dynamics file or of several files created through the use of Restart Files.
Index Sequentially	Assigns sequential numbers 1 through n, where n is the total number of datasets in the animation, to the datasets for constructing the animation. This method must be used for animations composed of dynamics files from different runs.
Dataset Range	Consists of two fields, From and To, defining the first and last datasets of the range to be displayed. The lower limit for the From field is the first dataset in the animation. The upper limit for the To field is the last dataset in the animation.
Step Size	Specifies the step interval, which must be an integral multiple of the output frequency.
Clock Speed	Determines the initial rate at which the program cycles through the display of the frames in the dynamics animation when Clock or Cycle is selected from the Dynamics Animation palette. The default speed is 100. Interactive control of the speed is provided in the Dynamics emulator dial set (dial set 8).
Number Steps to Average Over	Controls the averaging of the displayed molecule from the trajectory files and is a simple mechanism for removing high-frequency motions in an animation. This allows more extensive and concerted motions to be visualized.
Regenerate Hydrogen Bonds	Causes hydrogen bonds to be generated for each frame of a subsequently created animation.
Regenerate Selections and Hydrogen Bonds	Controls current display and color selections applied to each frame of a subsequently created animation. Selecting this option also calculates hydrogen bonds on a frame-by-frame basis during creation of the animation. This option is needed, for example, for coloring by atom property.
Pack Atoms into Cell	Specifies that a molecular structure created by the Amorphous Builder application to be displayed in a unit cell.
Display Atom Labels	Specifies that labels are to be generated for each frame of an animation according to the currently defined atom labeling regime.
Display Geometry Monitors	Specifies that distance, angle, and torsion monitors are to be displayed for each frame of a dynamics animation. The distances, angles, and torsions are designated before creating the animation, with the tools on the Geometry palette.
Display Trails	Causes trails to be generated in frames of a subsequently created animation. Trails are vectors representing the last three positions of each atom in a frame of an animation. The vectors are drawn in display color 14 and appear as traces of atom movements.
Display Energy Trace	Specifies that a trace of the energy and temperature of the molecule throughout the dynamics simulation be displayed in the animation.
Do Not Display Dipole	Specifies that no dipole be displayed during animation.
Display Dipole for Whole Molecule	Specifies that a dipole in the form of a vector arrow be displayed for the molecule in each frame of the animation.
Display Dipole for Each Residue	Specifies that a dipole in the form of a vector arrow be displayed for each residue in each frame of the animation

An animation may be displayed frame-by-frame or continuously (like a movie). As each frame is displayed in the viewing area, its frame number is shown above the Dynamics dial. Frames may be displayed either forward or backward.

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Sample procedure - Dynamics animation

Complete the following exercise to become familiar with procedures in the Dynamics Animation application. The exercise uses the trajectory files generated in the previous section of this chapter.

1.   Start Dynamics Animation.

Display the Applications menu. Select Dynamics Animation.

The Dynamics Animation palette and Dial emulators are displayed. The filename of the current MSF (mypeptide.msf) is displayed in the top left corner of the viewing area. However, the structure is not displayed until the animation is created.

2.   Select coordinate trajectory files.

From the Dynamics Animation palette, select Select Trajectories. A dialog box is displayed offering options for the management of coordinate trajectory files to be displayed.

Select the option:

Initialize Dynamics Files

Select the OK button. A File Librarian dialog box is displayed.

Select the file mypep_h.DCD, created during the dynamics heating phase.

Select the Open button. Information contained in the .DCD file is displayed in the textport. The dialog box offering options for the management of coordinate trajectories is redisplayed.

Select the option:

Add a File

Select the OK button. A File Librarian dialog box is redisplayed.

Select the file mypep_e.DCD, created during the equilibration phase of the dynamics run.

Select the Open button. Information contained in the .DCD file is displayed in the textport, and the dialog box offering options for the management of coordinate trajectories is redisplayed.

Select the option:

Add a File

Select the OK button. The File Librarian dialog box is redisplayed.

Select the file mypep_s.DCD, created during the dynamics simulation phase.

Select the Open button. Information contained in the .DCD file is displayed in the textport. A dialog box offering options for the management of coordinate trajectories is redisplayed.

Select the option:

List Current Files

Select the OK button.

The three .DCD files are listed in the textport:

Dynamics file: 1 mypep_h.DCD
Dynamics file: 2 mypep_e.DCD
Dynamics file: 3 mypep_s.DCD

The dialog box offering options for the management of coordinate trajectories is redisplayed.

3.   Display the header information for the selected .DCD files.

Select the option:

Show File Headers

Select the OK button. A dialog box is displayed allowing the selection of trajectory files to be read.

Enter the values:

Enter the first number in range: 1
Enter the last number in range: 3

Select the OK button. The header for each of the three trajectory files is displayed in the textport.

file no. 1 is of type CORD
The icntrl array is:
60 10 10 600 10 0 0 558 0 0.02045
number of datasets: 60
starting dataset: 10
ending dataset: 600
step size: 10
no of fixed atoms: 0
*** TITLE CARD READ FOR FILE UNIT - 3
* MINIMIZED COORDINATESFROM CHARMM
* DATE: 6/17/91 9:47:31 CREATED BY USER:emily

file no. 2 is of type CORD
The icntrl array is:
60 610 10 600 10 0 0 558 0 0.02045
number of datasets: 60
starting dataset: 610
ending dataset: 1200
step size: 10
no of fixed atoms: 0
*** TITLE CARD READ FOR FILE UNIT - 3
* COORDINATES AFTER HEATING DYNAMICS
* DATE: 6/17/91 9:56:26 CREATED BY USER:emily

file no. 3 is of type CORD
The icntrl array is:
60 1210 10 600 10 0 0 558 0 0.02045
number of datasets: 60
starting dataset: 1210
ending dataset: 1800
step size: 10
no of fixed atoms: 0
*** TITLE CARD READ FOR FILE UNIT - 3
* COORDINATES AFTER EQUILIBRATION DYNAMICS
* DATE: 6/17/91 10: 8:1 CREATED BY USER:emily

A dialog box offering options for the management of coordinate trajectories is redisplayed. Select the Exit button in the dialog box. The box is removed from the screen.

4.   Select animation specifications.

From the Dynamics Animation palette, select Set Up Animation. A dialog box is displayed that is used to define how the trajectory is displayed.

Select the option:

Use CHARMm Header

Enter the values:

From: 10
To: 1800
Step Size: 10
Clock Speed: 100.0
Number Steps to Average over: 0

Select the options:

Regenerate Hydrogen Bonds
Display Trails
Do not display dipole

Select the OK button. The dialog box is removed from the screen.

5.   Create the animation.

From the Dynamics Animation palette, select Create Animation. The selection is checked and highlighted. The dynamics trajectory is displayed frame by frame. Hydrogen bonds for the conformation are calculated and displayed in the frame.

The frame number is displayed above the dynamics emulator dial in the Dial Emulator window. The progress of the creation is displayed in both the message line and the textport.

When the creation is finished, the first frame is displayed in the viewing area. The dynamics emulator dials are activated, and frame number 10 is displayed over the Dynamics emulator dial.

6.   Step through several frames.

Place the cursor on the plus sign (+) in the Dynamics dial emulator box. Press and hold the left mouse button. Each trajectory frame is displayed in ascending order until the mouse button is released or the end of the trajectory is reached. The frame number in the Dynamics dial changes to reflect the frame in view.

Use the minus (-) button in the Dynamics dial box to display the frames in descending order.

7.   Display frames continuously

From the Dynamics Animation palette, select Clock. The selection is checked and highlighted. The animation movie is continuously displayed in the forward direction until the last frame is reached. The movie immediately jumps back to the first frame and repeats the display until Clock is deselected.

8.   Adjust the speed of the display.

Place the cursor on the D of the Speed dial emulator. Press and hold the left mouse button. Release the mouse button. The speed value stops changing. and the display step rate increases to a higher value.

Press and hold the left mouse button. Release the mouse button. The speed value stops changing and the display step rate decreases to a lower value.

9.   Turn off the Clock tool.

From the Dynamics Animation palette select Clock. The tool is turned off and the continuous display of the trajectory is stopped.

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Create an animation with an energy trace

An energy trace plots the energy and temperature of the molecule throughout a dynamics simulation. The following exercise sets up an energy trace for the mypeptide animation.

1.   Select animation specifications.

From the Dynamics Animation palette, select Set Up Animation. A dialog box is displayed offering options for displaying the trajectory.

Select the option:

Use CHARMm Header

Enter the values:

From: 10
To: 1800
Step Size: 10
Clock Speed: 100.0
Number Steps to Average over: 0

Select the option:

Regenerate Hydrogen Bonds
Display Trails
Display Energy Trace
Do not display dipole

Select the Create button. A dialog box is displayed offering choices for the energy values to display.

Select the options:

Total Energy
Temperature

The animation is created. As each frame of the dynamics trajectory is displayed, the corresponding energy trace is displayed in a graph near the top of the viewing area. Energy Trace is checked and highlighted.

2.   Cycle through all of the frames.

From the Dynamics Animation palette, select Cycle. The trajectory is continuously displayed: first forward until the last frame is reached, then backward until the first frame is reached, then forward again until the selection is turned off. When each frame of the trajectory is displayed, the energy trace graph and the frame number are updated.

Select Cycle again. The selection is turned off and the continuous display of the trajectory is stopped.

3.   Examine structures associated with energy trace values.

Move the mouse so the cursor is over any point in the energy trace. Click the left mouse button. The energy trace cursor is moved to this location and the conformation corresponding to the selected energy trace values is displayed in the viewing area.

4.   Exit Dynamics Animation.

From the Dynamics Animation palette, select Exit Dynamics Animation. The palette, energy trace, and animation graphics are removed from the display. The structure mypeptide.msf is redisplayed in the viewing area.

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Summary

CHARMm dynamics simulates the natural motion of a molecular system and produces a set of coordinates and velocities that describe the atomic motions of the system over time. The resulting dynamics trajectory can be viewed in the Dynamics Animation application and analyzed in the Analysis application.

A typical molecular dynamics run involves heating, equilibration, and simulation. Parameters are set for each step in a run. Molecular dynamics simulations are usually computed at room temperature.

Equilibration is achieved by allowing the molecular system to evolve spontaneously for a period of time, integrating the equations of motion until the average temperature and structure remain stable. The procedure is continued until the statistical properties of the system become independent of time. Equilibration temperature must correspond to the final temperature used in heating.

Simulation takes an equilibrated structure as its starting point and produces a dynamics trajectory. In a typical simulation, the trajectory traces the motions of the macromolecule for a specified time. The simulation temperature must correspond to the equilibration temperature.

Dynamics heating and equilibration are usually performed only once on a molecular structure. Simulation may be run several times to show changes in the conformation of the molecule over time.

All coordinates calculated during a dynamics run are stored in the coordinate trajectory file specified in the dynamics setup. Each set of coordinates in the dynamics trajectory can be viewed using the Dynamics Animation application. You also can read data into an individual MSF. The final set of coordinates is stored in CHARMm external format at the end of the calculation.

With the Dynamics Animation application, you can interactively display a dynamics trajectory calculated by CHARMm, CNX, or X-PLOR. Displays can include a graphical representation of hydrogen bonding, interatomic distances, atomic positions, molecule energy, or atomic properties.

The dynamics trajectory calculated in CHARMm consists of datasets of atom coordinates written periodically. If the trajectory is thought of as a movie, then each individual dataset may be considered a frame. You can display the trajectory frames at any desired speed. Single frames may be saved to individual MSFs that can be compared in detail using the Molecular Similarity application.

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References

1.   Charles Brooks III, Martin Karplus, and B. M. Pettitt. 1988. Proteins: A Theoretical Perspective Of Dynamics, Structure And Thermodynamics. Advances in Chemical Physics. John Wiley and Sons, New York.

© 2006 Accelrys Software Inc.