8.3 NAMD calculation

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats (from J. of Compt. Chem. Vol. 26 (16), 1781-1802, 2005).
VEGA ZZ integrates in its environment the powerful capabilities of NAMD to perform molecular dynamics and energy minimizations in interactive mode. The graphic user interface allows to access to NAMD configuration in easy way and the 3D view permits to show the structural changes during the simulation by IMD interface (Interactive Molecular Dynamics). Through the included pre-settings, the users with a very basic knowledge of the MD theory can perform simulations and analyze the results as explained in the Trajectory analysis section.
Nevertheless, it's strongly recommended to consult the NAMD User Guide available at Theoretical and Computational Biophysics Group to understand better the MD concepts and the meaning of the parameter fields accessible by the graphic interface.
Selecting Calculate NAMD in the main menu or clicking the icon in the left toolbar, NAMD dialog window is shown.
Some information included in this manual section, are from NAMD User Guide.

 

8.3.1 Before to run a NAMD simulation

Before to start a NAMD calculation, the molecule that you want to undergo to the simulation must be prepared:

WARNING:
not all atom types are supported by NAMD: you can use CHARMM22_LIG (includes parameters for small molecules, proteins and nucleic acids), CHARMM22_LIPID (for lipids only), CHARMM22_NA (for nucleic acids only), CHARMM22_PROT (for proteins only) and OPLS. The CHARMM force field can be used only if you have the Accelrys' parm.prm file in the ...\VEGA ZZ\Data\Parameters directory that can't be included in the package for copyright reasons.

No special files are required to run the simulation (e.g. PDB and PSF files) because all needed ones are created by the interface.

 

8.3.2 NAMD interface basics

The interface is designed to remember the input fields/commands used in the standard NAMD input files: moving the mouse pointer over a field label a hint with the name of the NAMD command is shown.
Context menus are accessible making faster the page navigation:

 

Page popup menu

 

Clicking the right mouse button outside the page bars, the settings menu is shown:

 

Settings context menu

 

This menu allows to load (Load settings) or save (Save settings) the settings in standard NAMD configuration file format. Checking the Ignore file names, the commands having a file name as argument are ignored (this is useful to keep the file names in the dialog window). Selecting Default settings, all parameters are reverted to the default values.

 

8.3.3 Run modes and Interactive Molecular Dynamics (IMD)

The box at the top of NAMD dialog window allows to change the run mode and the IMD parameters:

 

Basic functions and Interactive Molecular Dynamics

 

The Run mode group set  how NAMD is started when the you click Run button:

In Interactive molecular dynamics box, checking Update graphics (correspondent to the IMDon NAMD command), you can enable the visualization of the structure changes in the 3D environment during the simulation. Frequency (IMDfreq) sets the graphic update frequency (e.g. 20 means that the graphic is updated every 20 simulation steps), TCP/IP port (IMDport) sets the communication port number between NAMD and VEGA ZZ. If the port is already in use by another application, its value is automatically increased until a free port is found. Checking Ignore forces (IMDignore), NAMD ignores the forces sent by the client application (VMD) for the steered molecular dynamics and checking Wait connection (IMDwait), NAMD stops itself in initialization phase until the connection with the client application is completed (VMD or VEGA ZZ).

 

8.3.4 Basic simulation parameters

In Calculation type box, you can choose to perform Conjugate gradients minimization, Velocity quenching minimization (not recommended) and Molecular dynamics.

 

8.3.4.1 Timestep parameters

 

8.3.4.2 Multiple timestep parameters

 

8.3.5 Input

In this page, you can set the input file name and the force field for the simulation.

 

Input

 

8.3.6 Output

This page allows to control the output parameters and the output file names.

 

Output

 

8.3.6.1 Output file parameters

 

8.3.7 Simulation space partitioning

Simulation space partitioning

 

8.3.8 Dynamics

Dynamics

 

8.3.9 PME - Particle Mesh Ewald

PME stands for Particle Mesh Ewald and is an efficient full electrostatics method for use with periodic boundary conditions. None of the parameters should affect energy conservation, although they may affect the accuracy of the results and momentum conservation.

 

PME - Particle Mesh Ewald

 

8.3.10 BC - Boundary Conditions

BC - Boundary Conditions

 

8.3.10.1 Spherical

NAMD provides spherical harmonic boundary conditions. These boundary conditions can consist of a single potential or a combination of two potentials. The following parameters are used to define these boundary conditions.

 

8.3.10.2 Cylindrical

NAMD provides cylindrical harmonic boundary conditions. These boundary conditions can consist of a single potential or a combination of two potentials. The following parameters are used to define these boundary conditions.

 

Cylindrical

 

8.3.10.3 Periodic

NAMD provides periodic boundary conditions in 1, 2 or 3 dimensions. The following parameters are used to define these boundary conditions.

 

Periodic

 

8.3.11 Constraints

Before to proceed with a constrained simulation, the constraint constants must be applied to the molecule. For more information, see the Atom constraints section.

 

Constraints

 

8.3.11.1 Harmonic constraints parameters

The following describes the parameters for the harmonic constraints feature of NAMD. Actually, this feature should be referred to as harmonic restraints rather than constraints, but for historical reasons the terminology of harmonic constraints has been carried over from X-PLOR. This feature allows a harmonic restraining force to be applied to any set of atoms in the simulation.

 

8.3.11.2 Fixed atoms parameters

Atoms may be held fixed during a simulation.

 

8.3.12 Temperature

Temperature

 

8.3.12.1 Langevin

NAMD is capable of performing Langevin dynamics, where additional damping and random forces are introduced to the system. This capability is based on that implemented in X-PLOR which is detailed in the X-PLOR User's Manual, although a different integrator is used.

 

8.3.12.2 Rescaling

NAMD allows equilibration of a system by means of temperature rescaling. Using this method, all of the velocities in the system are periodically rescaled so that the entire system is set to the desired temperature. The following parameters specify how often and to what temperature this rescaling is performed.

 

8.3.12.3 Coupling

NAMD is capable of performing temperature coupling, in which forces are added or reduced to simulate the coupling of the system to a heat bath of a specified temperature. This capability is based on that implemented in X-PLOR which is detailed in the X-PLOR User's Manual [7].

 

8.3.14.4 Reassignment

NAMD allows equilibration of a system by means of temperature reassignment. Using this method, all of the velocities in the system are periodically reassigned so that the entire system is set to the desired temperature. The following parameters specify how often and to what temperature this reassignment is performed.

 

8.3.13 Minimization

Minimization

 

8.3.13.1 Conjugate gradients parameters

The default minimizer uses a sophisticated conjugate gradient and line search algorithm with much better performance than the older velocity quenching method. The method of conjugate gradients is used to select successive search directions (starting with the initial gradient) which eliminate repeated minimization along the same directions. Along each direction, a minimum is first bracketed (rigorously bounded) and then converged upon by either a golden section search, or, when possible, a quadratically convergent method using gradient information.

 

8.3.13.2 Velocity quenching parameters

You can perform energy minimization using a simple quenching scheme. While this algorithm is not the most rapidly convergent, it is sufficient for most applications. There are only two parameters for minimization: one to activate minimization and another to specify the maximum movement of any atom.

 

8.3.14 Other

Other

 

In Other parameters box, you can put parameters not managed by graphic interface and TCL scripts. The Configurations box includes the gadgets to control the pre-settings: to configure NAMD, several commands can be involved and thus it could be useful to save the configuration more then one time. As explained in NAMD interface basics section, you can Load, Save and revert to Default configuration, pressing the buttons in the Configurations box or using the context menu. The Ignore file name checkbox has the same function of the homonymous item in the context menu: if it's checked, the fields containing file names aren't updated when the configuration is loaded, in order to preserve the names of the current molecule.
In the Presettings box, are shown the NAMD configuration files saved in the ...\VEGA ZZ\Data\NAMD directory with the .namd extension. They can be managed by the context menu displayed when you click with the right mouse button on a presetting in the list.

 

Menu item Description
Load Load the preset into the graphic interface
Save Save the preset to a new file.
Update Update the current preset with the new changes.
Edit Edit the preset in text mode (see the Mini Text Editor).
Rename Rename the preset.
Delete Delete the preset. A warning message is shown before proceeding.
Refresh list

Refresh the preset list. This function is useful if you added manually al preset file in the ...\VEGA ZZ\Data\NAMD directory and you want see it in the list without restarting VEGA ZZ.

 

8.3.15 Starting the simulation

Clicking Run button, the simulation starts: the PDB file is created with constraints parameters if required, the PSF topology file is built and the NAMD command file as generated by the data fitted in the graphic interface fields. All files are saved in the directory in which the current molecule is loaded or saved.
Before to run NAMD, VEGA ZZ performs an extra check to verify if all parameters are included in the force field data (the files are placed in ...\VEGA ZZ\Data\Parameters directory). It may be possible, especially for the small molecules, that certain parameters (bonds, angles, torsions, impropers) are missing and the Missing parameter table is shown. Thanks to this table, you can put the required parameters.