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:

• it must be completed (check hydrogens and connectivity). The bond order isn't used by NAMD and so it can remain unassigned (remember that AMMP has a completely different behaviour: it requires the bond order to calculate the force constants);
   
• the atom charges must be assigned/calculated (see Charges and potential and Mopac for small molecules);
   
• all atoms must have the correct atom type that can be assigned manually (Charges and potential) or automatically by NAMD interface. The automatic assignment is enabled when the interface finds atom type unassigned or included in a force field that differs from that you selected in the dialog window;
   
• is not possible to perform simulations even if one atom has an unassigned potential. They are highlighted when you assign the atom types with the Charges and potential function with the question mark label (?) or showing the atom types labels (View Label atom Type in main menu).

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:

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

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:

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

• Run NAMD in interactive mode.
  It's the default operation mode. VEGA ZZ creates a process attached to NAMD and if the IMD is enabled, the 3D graphic is updated during the simulation. When VEGA ZZ is closed, the NAMD process is killed and the simulation aborts.
   
• Run NAMD as separated process.
  VEGA ZZ creates a detached process for NAMD. No graphic update is possible, but the calculation isn't killed if VEGA ZZ is closed.
   
• Prepare the input files only.
  Choosing this option, the NAMD input files are created without to start the calculation. That's useful to prepare one or more calculations for batch run. In the directory where the files are placed, a file with the calculation prefix and the .cmd extension as name is saved and executing it, you can start the calculation.

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

• Number of timesteps - numsteps
  The number of simulation timesteps to be performed.
   
• Timestep size (fs) - timestep
  The timestep size to use when integrating each step of the simulation. The value is specified in femtoseconds.
   
• Starting timestep value - firsttimestep
  The number of the first timestep. This value is typically used only when a simulation is a continuation of a previous simulation. In this case, rather than having the timestep restart at 0, a specific timestep number can be specified.
   
• Timesteps per cycle - stepspercycle
  Number of timesteps in each cycle. Each cycle represents the number of timesteps between atom reassignments.

8.3.4.2 Multiple timestep parameters

• Timesteps between full elect. evaluations - fullElectFrequency
  This parameter specifies the number of timesteps between each full electrostatics evaluation.
   
• Timesteps between nonbonded evaluations - nonbondedFreq
  This parameter specifies how often short-range non-bonded interactions should be calculated. Setting it between 1 and Timesteps between full elect. evaluations (fullElectFrequency) allows triple timestepping where, for example, one could evaluate bonded forces every 1 fs, short-range nonbonded forces every 2 fs, and long-range electrostatics every 4 fs.
   
• MTS algirithm type - MTSAlgorithm
  Specifies the multiple timestep algorithm used to integrate the long and short range forces. Impulse/VerletI is the same as r-RESPA and Constant/Naive is the stale force extrapolation method.
   
• Long and short range forces split - longSplitting
  Specifies the method used to split electrostatic forces between long and short range potentials. It can be C1 (default) or Xplor. For more details, see the NAMD NAMD User Guide.
   
• Modified impulse method (MOLLY) - molly
  This method eliminates the components of the long range electrostatic forces which contribute to resonance along bonds to hydrogen atoms, allowing Timesteps between full elect. evaluations (fullElectFrequency) of 6 (vs. 4) with a 1 fs timestep without using ShakeH type all (rigidBonds all). You may use rigidBonds water but using ShakeH type all (rigidBonds all) with MOLLY makes no sense since the degrees of freedom which MOLLY protects from resonance are already frozen.
   
• Tolerance for MOLLY errors - mollyTolerance
  Convergence criterion for MOLLY algorithm.
   
• Max. MOLLY iterations - mollyIterartions
  Maximum number of iterations for MOLLY algorithm.

8.3.5 Input

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

• Automatic input
  Checking the Automatic input (default) the fields are automatically filled using the molecule name in the current workspace.
   
• Force field
  Force field that will be used in the simulation. The combo-box is automatically updated when the dialog window is shown, reading the list of the parameter files in the ...\VEGA ZZ\Data\ with the .inp extension.
   
• Coordinate PDB file - coordinates
  The PDB file containing initial position coordinate data.
   
• Binary PDB file - bincoordinates
  PDB binary file used to restart the calculation.
   
• Parameter file - parameters
  A parameter file defining all or part of the parameters necessary for the molecular system to be simulated. You can specify more then one parameter file separating them by a space character. The file requester allows multiple selection.
   
• Format - paraTypeXplor, paraTypeCharmm
  Specifies if the parameter file is in CHARMM or Xplor format.
   
• Velocities file - velocities, binvelocities
  It's the PDB file containing the initial velocities for all atoms in the simulation. This is typically a restart file or final velocity file written by NAMD during a previous simulation.
   
• Binary velocities
  If it's checked, the Velocities file is in binary format.

8.3.6 Output

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

• Output file - outputname
  At the end of every simulation, NAMD writes two PDB files: the former containing the final coordinates and the latter containing the final velocities of all atoms in the simulation. This option specifies the file prefix for these two files. The position coordinates will be saved to a file named as this prefix with .coor appended. The velocities will be saved to a file named as this prefix and with .vel suffix.
   
• Output frequency - outputEnergies
  The number of timesteps between each energy output of NAMD. This value specifies how often NAMD should output the current energy values. By default, this is done every step. For long simulations, the amount of output generated by NAMD can be greatly reduced by outputting the energies only occasionally.
   
• Binary output - binaryoutput
  Activates the use of binary output files. If this option is set to Yes, then the final output files will be written in binary rather than PDB format. Binary files preserve more accuracy between NAMD restarts than ASCII PDB files, but the binary files are not guaranteed to be transportable between computer architectures.
   
• Trajectory file - DCDfile
  The binary DCD position coordinate trajectory filename. This file stores the trajectory of all atom position coordinates using the same format (binary DCD) as X-PLOR.
   
• Trajectory frequency - DCDfreq
  The number of timesteps between the writing of position coordinates to the trajectory file. The initial positions will not be included in the trajectory file.
   
• Velocity trajectory file - velDCDfile
  The binary DCD velocity trajectory filename. This file stores the trajectory of all atom velocities using the same format (binary DCD) as X-PLOR.
   
• Velocity frequency - velDCDfreq
  The number of timesteps between the writing of velocities to the trajectory file. The initial velocities will not be included in the trajectory file.
   
• Restart file prefix - restartname
  The prefix to use for restart filenames. NAMD produces PDB restart files that store the current positions and velocities of all atoms at some step of the simulation. This option specifies the prefix to use for restart files.
   
• Restart frequency - restartfreq
  The number of timesteps between the generation of restart files.
   
• Binary restart - binaryrestart
  Activates the use of binary restart files. If this option is checked, then the restart files will be written in binary rather than PDB format. Binary files preserve more accuracy between NAMD restarts than ASCII PDB files, but the binary files are not guaranteed to be transportable between computer architectures.
   
• Remove files after minimization
  Checking it, all output files generated by minimization are removed. This option has no effects if you are performing a MD simulation.
   
• Timestep in restart - restartsave
  Appends the current timestep to the restart filename prefix, producing a sequence of restart files rather than only the last version written.
   
• Write unit cell data - DCDUnitCell
  If this option is set to Yes, then DCD files will contain unit cell information in the style of CHARMM DCD files.

8.3.6.1 Output file parameters

• Add crossterm energy to dihedral - mergeCrossterms
  If crossterm (or CMAP) terms are present in the potential, the energy is added to the dihedral energy to avoid altering the energy output format.
   
• Momentum output frequency - outputMomenta
  The number of timesteps between each momentum output of NAMD. If specified and nonzero, linear and angular momenta will be printed to the output.
   
• Pressure output frequency - outputPressure
  The number of timesteps between each pressure output of NAMD. If specified and nonzero, atomic and group pressure tensors will be printed to the output.
   
• Timing output frequency - outputTiming
  The number of timesteps between each timing output of NAMD. If nonzero, CPU and wallclock times and memory usage will be printed to the output.

8.3.7 Simulation space partitioning

• Cutoff (Å) - cutoff
  Cutoff value for non-bond energy evaluation.
   
• Switching function - switching
  If switching function is specified to be Off, then a truncated cutoff is performed. If switching function is turned on, then smoothing functions are applied to both the electrostatics and Van der Waals forces.
   
• Activation switching distance - switchdist
  Distance at which the switching function should begin to take effect. This parameter only has meaning if the switching function is set to On.
   
• Max. distance for limit interaction (Å) - limitdist
  The electrostatic and Van der Waals potential functions diverge as the distance between two atoms approaches zero. The potential for atoms closer than limitdist is instead treated as ar² + c with parameters chosen to match the force and potential at limitdist. This option should primarily be useful for alchemical free energy perturbation calculations, since it makes the process of creating and destroying atoms far less drastic energetically. The larger the value of limitdist the more the maximum force between atoms will be reduced. In order to not alter the other interactions in the simulation, limitdist should be less than the closest approach of any non-bonded pair of atoms; 1.3 Å appears to satisfy this for typical simulations but the user is encouraged to experiment. There should be no performance impact from enabling this feature.
   
• Distance for inclusion in pair list (Å) - pairlistdist
  A pair list is generated pairlistsPerCycle times each cycle, containing pairs of atoms for which electrostatics and Van der Waals interactions will be calculated. This parameter is used when switching is set to on to specify the allowable distance between atoms for inclusion in the pair list. This parameter is equivalent to the X-PLOR parameter CUTNb. If no atom moves more than pairlistdist - cutoff during one cycle, then there will be no jump in electrostatic or Van der Waals energies when the next pair list is built. Since such a jump is unavoidable when truncation is used, this parameter may only be specified when switching is set to on. If this parameter is not specified and switching is set to on, the value of cutoff is used. A value of at least one greater than cutoff is recommended.
   
• How to assign atoms to patches - splitpatch
  When set to hydrogen, hydrogen atoms are kept on the same patch as their parents, allowing faster distance checking and rigid bonds.
   
• Group-based distance testing (Å) - hgroupCutoff
  This should be set to twice the largest distance which will ever occur between a hydrogen atom and its mother. Warnings will be printed if this is not the case. This value is also added to the margin.
   
• Extra length in patch dimension (Å) - margin
  An internal tuning parameter used in determining the size of the cubes of space with which NAMD uses to partition the system. The value of this parameter will not change the physical results of the simulation. Unless you are very motivated to get the very best possible performance, just leave this value at the default.
   
• Min. procs for pairlist - pairlistMinProcs
  Pairlists may consume a large amount of memory as atom counts, densities, and cutoff distances increase. Since this data is distributed across processors it is normally only problematic for small processor counts. Set this parameter to the smallest number of processors on which the simulation can fit into memory when pairlists are used.
   
• Regenerate x times per cycle - pairlistsPerCycle
  Rather than only regenerating the pairlist at the beginning of a cycle, regenerate multiple times in order to better balance the costs of atom migration, pairlist generation, and larger pairlists.
   
• How often to print warnings - outputPairlists
  If an atom moves further than the pairlist tolerance during a simulation (initially (pairlistdist - cutoff)/2 but refined during the run) any pairlists covering that atom are invalidated and temporary pairlists are used until the next full pairlist regeneration. All interactions are calculated correctly, but efficiency may be degraded. Enabling this parameter will summarize these pairlist violation warnings periodically during the run.
   
• Tolerance reduction fraction - pairlistShrink
  In order to maintain validity for the pairlist for an entire cycle, the pairlist tolerance (the distance an atom can move without causing the pairlist to be invalidated) is adjusted during the simulation. Every time pairlists are regenerated the tolerance is reduced by this fraction.
   
• Tolerance increasing fraction - pairlistGrow
  In order to maintain validity for the pairlist for an entire cycle, the pairlist tolerance (the distance an atom can move without causing the pairlist to be invalidated) is adjusted during the simulation. Every time an atom exceeds a trigger criterion that is some fraction of the tolerance distance, the tolerance is increased by this fraction.
   
• Tolerance trigger - pairlistTrigger
  The goal of pairlist tolerance adjustment is to make pairlist invalidations rare while keeping the tolerance as small as possible for best performance. Rather than monitoring the (very rare) case where atoms actually move more than the tolerance distance, we reduce the trigger tolerance by this fraction. The tolerance is increased whenever the trigger tolerance is exceeded, as specified by pairlistGrow.

8.3.8 Dynamics

• Exclusion policy - exclude
  This parameter specifies which pairs of bonded atoms should be excluded from non-bonded interactions. With the value of none, no bonded pairs of atoms will be excluded. With the value of 1-2, all atom pairs that are directly connected via a linear bond will be excluded. With the value of 1-3, all 1-2 pairs will be excluded along with all pairs of atoms that are bonded to a common third atom (i.e., if atom A is bonded to atom B and atom B is bonded to atom C, then the atom pair A-C would be excluded). With the value of 1-4, all 1-3 pairs will be excluded along with all pairs connected by a set of two bonds (i.e., if atom A is bonded to atom B, and atom B is bonded to atom C, and atom C is bonded to atom D, then the atom pair A-D would be excluded). With the value of scaled1-4, all 1-3 pairs are excluded and all pairs that match the 1-4 criteria are modified. The electrostatic interactions for such pairs are modified by the constant factor defined by 1-4scaling. The van der Waals interactions are modified by using the special 1-4 parameters defined in the parameter files.
   
• Temperature (K) - temperature
  Initial temperature value for the system. Using this option, a random velocity distribution will be generated for the initial velocities for all the atoms such that the system is at the desired temperature.
   
• Allow initial center of mass motion - COMmotion
  Specifies whether or not motion of the center of mass of the entire system is allowed. If this option is set to No, the initial velocities of the system will be adjusted to remove center of mass motion of the system. Note that this does not preclude later center-of-mass motion due to external forces such as random noise in Langevin dynamics, boundary potentials, and harmonic restraints.
   
• Remove center of mass drift for PME - zeroMomentum
  If enabled, the net momentum of the simulation and any resultant drift is removed before every full electrostatics step. This correction should conserve energy and have minimal impact on parallel scaling. This feature should only be used for simulations that would conserve momentum except for the slight errors in PME (Features such as fixed atoms, harmonic restraints, steering forces, and Langevin dynamics do not conserve momentum; use in combination with these features should be considered experimental). Since the momentum correction is delayed, enabling outputMomenta will show a slight nonzero linear momentum but there should be no center of mass drift.
   
• Dielectric constant - dielectric
  Dielectric constant for the system. A value of 1.0 implies no modification of the electrostatic interactions. Any larger value will lessen the electrostatic forces acting in the system.
   
• Scaling factor for nonbonded forces - nonbondedScaling
  Scaling factor for electrostatic and Van der Waals forces. A value of 1.0 implies no modification of the interactions. Any smaller value will lessen the non-bonded forces acting in the system.
   
• Scaling factor for 1-4 interactions - 1-4scaling
  Scaling factor for 1-4 interactions. This factor is only used when the Exclusion policy (exclude) parameter is set to scaled1-4. In this case, this factor is used to modify the electrostatic interactions between 1-4 atom pairs. If the exclude parameter is set to anything but scaled1-4, this parameter has no effect regardless of its value.
   
• Use geometric mean for L-J sigmas - vdwGeometricSigma
  Use geometric mean, as required by OPLS, rather than traditional arithmetic mean when combining Lennard-Jones sigma parameters for different atom types.
   
• Random number seed - seed
  Number used to seed the random number generator if temperature or langevin is selected. This can be used so that consecutive simulations produce the same results. If no value is specified, NAMD will choose a pseudo-random value based on the current UNIX clock time. The random number seed will be output during the simulation startup so that its value is known and can be reused for subsequent simulations. Note that if Langevin dynamics are used in a parallel simulation (i.e., a simulation using more than one processor) even using the same seed will not guarantee reproducible results.
   
• ShakeH type - rigidBonds
  When water is selected, the hydrogen-oxygen and hydrogen-hydrogen distances in waters are constrained to the nominal length or angle given in the parameter file, making the molecules completely rigid. When this parameter is all, waters are made rigid as described above and the bond between each hydrogen and the (one) atom to which it is bonded is similarly constrained. For the default case none, no lengths are constrained.
   
• Bond-length error for ShakeH (Å) - rigidTolerance
  The ShakeH algorithm is assumed to have converged when all constrained bonds differ from the nominal bond length by less than this amount.
   
• Max. ShakeH iterations - rigidIterations
  The maximum number of iterations ShakeH will perform before giving up on constraining the bond lengths. If the bond lengths do not converge, a warning message is printed, and the atoms are left at the final value achieved by ShakeH. Although the default value is 100, convergence is usually reached after fewer than 10 iterations.
   
• Exit if a ShakeH error occurs - rigidDieOnError
  Exits and reports an error if rigidTolerance is not achieved after rigidIterations.
   
• Use SETTLE for waters - useSETTLE
  If rigidBonds are enabled then use the non-iterative SETTLE algorithm to keep waters rigid rather than the slower SHAKE algorithm.

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.

• Use Particle Mesh Evald - PME
  Turns on Particle Mesh Ewald.
   
• PME direct space tolerance - PMETolerance
  Affects the value of the Ewald coefficient and the overall accuracy of the results.
   
• PME interpolation order - PMEInterpOrder
  Charges are interpolated onto the grid and forces are interpolated off using this many points, equal to the order of the interpolation function plus one.
   
• Max. space between grid points - PMEGridSpacing
  The grid spacing partially determines the accuracy and efficiency of PME. If any of the grid sizes below are not set, then PMEGridSpacing must be set (recommended value is 1.0 Å) and will be used to calculate them. If a grid size is set, then the grid spacing must be at least PMEGridSpacing (if set, or a very large default of 1.5).
   
• Number of grid points in X dimension - PMEGridSizeX
  Number of grid points in Y dimension - PMEGridSizeY
  Number of grid points in Z dimension - PMEGridSizeZ
  The grid size partially determines the accuracy and efficiency of PME. For speed, the value should have only small integer factors (2, 3 and 5). To fix values to be factors of 2, 3 and 5, you can click the Fix buttons. To calculate automatically the grid points, you can click the Calculate button.
   
• Processors for FFT and recip. sum - PMEProcessors
  For best performance on some systems and machines, it may be necessary to restrict the amount of parallelism used. Experiment with this parameter if your parallel performance is poor when PME is used.
   
• Estimate to optimize FFTW - FFTWEstimate
  Do not optimize FFT based on measurements, but on FFTW rules of thumb. This reduces startup time, but may affect performance.
   
• Use FFTW wisdom archive fie - FFTWUseWisdom
  Try to reduce startup time when possible by reading FFTW ``wisdom'' from a file, and saving wisdom generated by performance measurements to the same file for future use. This will reduce startup time when running the same size PME grid on the same number of processors as a previous run using the same file.
   
• Wisdom file - FFTWWisdomFile
  File where FFTW wisdom is read and saved. If you only run on one platform this may be useful to reduce startup times for all runs. The default is likely sufficient, as it is version and platform specific.
   
• Calculate full electrostatic directly - FullDirect
  Specifies whether or not direct computation of full electrostatics should be performed.

8.3.10 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.

• Enabled - sphericalBC
  Specifies whether or not spherical boundary conditions are to be applied to the system.
   
• Center - sphericalBCCenter
  Location around which sphere is cantered. Clicking the calculator button, the fields are automatically filled with the center of mass of the molecule.
   
• 1st radius (Å) - sphericalBCr1
  Distance at which the first potential of the boundary conditions takes effect. This distance is a radius from the center. Clicking the calculator button, the field is automatically filled with the the radius of the hypothetical sphere containing the molecule.
   
• 1st force constant - sphericalBCk1
  Force constant for the first harmonic potential. A positive value will push atoms toward the center, and a negative value will pull atoms away from the center.
   
• 1st exponent - sphericalBCexp1
  Exponent for first boundary potential. The only likely values to use are 2 and 4.
   
• 2nd radius (Å) - sphericalBCr2
  Distance at which the second potential of the boundary conditions takes effect. This distance is a radius from the center. Clicking the calculator button, the field is automatically filled with the the radius of the hypothetical sphere containing the molecule.
   
• 2nd force constant - sphericalBCk2
  Force constant for the second harmonic potential. A positive value will push atoms toward the center, and a negative value will pull atoms away from the center.
   
• 2nd exponent - sphericalBCexp2
  Exponent for second boundary potential. The only likely values to use are 2 and 4.

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.

• Enabled - cylindricalBC
  Specifies whether or not cylindrical boundary conditions are to be applied to the system.
   
• Center - cylindricalBCCenter
  Location around which cylinder is cantered. Clicking the calculator button, the fields are automatically filled with the center of mass of the molecule.
   
• Cylinder axis alignment - cylinderBCAxis
  Axis along which cylinder is aligned.
   
• 1st radius (Å) - cylindricalBCr1
  Distance at which the first potential of the boundary conditions takes effect along the non-axis plane of the cylinder. Clicking the calculator button, the field is automatically filled with the the radius of the hypothetical sphere containing the molecule.
   
• 1st distance (Å) - cylindricalBCl1
  Distance at which the first potential of the boundary conditions takes effect along the cylinder axis.
   
• 1st force constant - cylindricalBCk1
  Force constant for the first harmonic potential. A positive value will push atoms toward the center, and a negative value will pull atoms away from the center.
   
• 1st exponent - cylindricalBCexp1
  Exponent for first boundary potential. The only likely values to use are 2 and 4.
   
• 2nd radius (Å) - cylindricalBCr2
  Distance at which the second potential of the boundary conditions takes effect along the non-axis plane of the cylinder. Clicking the calculator button, the field is automatically filled with the the radius of the hypothetical sphere containing the molecule.
   
• 2st distance (Å) - cylindricalBCl2
  Distance at which the second potential of the boundary conditions takes effect along the cylinder axis.
   
• 2nd force constant - cylindricalBCk2
  Force constant for the second harmonic potential. A positive value will push atoms toward the center, and a negative value will pull atoms away from the center.
   
• 2nd exponent - cylindricalBCexp2
  Exponent for second boundary potential. The only likely values to use are 2 and 4.

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.

• Enabled
  Enables the periodic boundary conditions.
   
• Basis vector 1 - cellBasisVector1
  Basis vector 2 - cellBasisVector2
  Basis vector 3 - cellBasisVector3
  They specify the basis vectors for periodic boundary conditions. Clicking the calculator button, all fields are filled with the cell dimensions of the molecule.
   
• Cell origin - cellOrigin
  When position rescaling is used to control pressure, this location will remain constant. Also used as the center of the cell for wrapped output coordinates. Clicking the calculator button, the fields are filled with the mass center of the molecule.
   
• XSC file name - extendedSystem
  In addition to .coor and .vel output files, NAMD generates a .xsc (eXtended System Configuration) file which contains the periodic cell parameters and extended system variables, such as the strain rate in constant pressure simulations. Periodic cell parameters will be read from this file if this option is present, ignoring the above parameters.
   
• XST trajectory - XSTfile
  NAMD can also generate a .xst (eXtended System Trajectory) file which contains a record of the periodic cell parameters and extended system variables during the simulation.
   
• Frequency - XSTfreq
  Controls how often the extended system configuration will be appended to the XST file.
   
• Wrap water - wrapWater
  Coordinates are normally output relative to the way they were read in. Hence, if part of a molecule crosses a periodic boundary it is not translated to the other side of the cell on output. This option alters this behaviour for water molecules only.
   
• Wrap all - wrapAll
  Coordinates are normally output relative to the way they were read in. Hence, if part of a molecule crosses a periodic boundary it is not translated to the other side of the cell on output. This option alters this behavior for all contiguous clusters of bonded atoms.
   
• Wrap nearest - wrapNearest
  Coordinates are normally wrapped to the diagonal unit cell centered on the origin. This option, combined with wrapWater or wrapAll, wraps coordinates to the nearest image to the origin, providing hexagonal or other cell shapes.

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.

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.

• Constraints - constraints
  Specifies whether or not harmonic constraints are active. If it is set to Off, then no harmonic constraints are computed.
   
• Constraint exponent - consexp
  Exponent to be use in the harmonic constraint energy function.
   
• Constants file - conskfile
  PDB file to use for force constants for harmonic constraints. By default, this field is filled with the PDB file name including the atom coordinates and generated automatically when the user presses the Run button.
   
• Ref. pos. file - consref
  PDB file to use for reference positions for harmonic constraints. Each atom that has an active constraint will be constrained about the position specified in this file. By default, this field is filled with the PDB file name including the atom coordinates and generated automatically when the user presses the Run button.
   
• PDB column with the force constants - conskcol
  Column of the PDB file to use for the harmonic constraint force constant. This parameter may specify any of the floating point fields of the PDB file, either X, Y, Z, occupancy, or beta-coupling (temperature-coupling). Regardless of which column is used, a value of 0 indicates that the atom should not be constrained. Otherwise, the value specified is used as the force constant for that atom's restraining potential. The default value is Beta-coupling (B) because it's the column used by VEGA ZZ to save the constraint constants.
   
• Scaling factor for energy function - constraintScaling
  The harmonic constraint energy function is multiplied by this parameter, making it possible to gradually turn off constraints during equilibration.
   
• Restraint the Cartesian coord. only - selectConstraints
  This option is useful to restrain the positions of atoms to a plane or a line in space. If active, this option will ensure that only selected Cartesian components of the coordinates are restrained. E.g.: Restraining the positions of atoms to their current z values with no restraints in X and Y will allow the atoms to move in the X-Y plane while retaining their original Z-coordinate. Restraining the X and Y values will lead to free motion only along the Z coordinate.
   
• X - selectConstrX
  Y - selectConstrY
  Z - selectConstrZ
  Restrain the Cartesian X, Y and Z components of the positions.

8.3.11.2 Fixed atoms parameters

Atoms may be held fixed during a simulation.

• Fixed atoms - fixedAtoms
  Specifies whether or not fixed atoms are present.
   
• Calculate forces between fixed atoms - fixedAtomsForces
  Specifies whether or not forces between fixed atoms are calculated. This option is required to turn fixed atoms off in the middle of a simulation. These forces will affect the pressure calculation, and you should leave this option off when using constant pressure if the coordinates of the fixed atoms have not been minimized. The use of constant pressure with significant numbers of fixed atoms is not recommended.
   
• Fixed atoms file - fixedAtomsFile
  PDB file to use for the fixed atom flags for each atom. If this parameter is not specified, then the PDB file specified by coordinates is used. By default, this field is filled with the PDB file name including the atom coordinates and generated automatically when the user presses the Run button.
   
• PDB column with fixed atoms - fixedAtomsCol
  Column of the PDB file to use for the containing fixed atom parameters for each atom. The coefficients can be read from any floating point column of the PDB file. A value of 0 indicates that the atom is not fixed. Regardless of which column is used, a value of 0 indicates that the atom should not be constrained. Otherwise, the value specified is used as the force constant for that atom's restraining potential. The default value is Beta-coupling (B) because it's the column used by VEGA ZZ to save the constraint constants.

8.3.12 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.

• Langevin dynamics - langevin
  Specifies whether or not Langevin dynamics active.
   
• Temperature (K) - langevinTemp
  Temperature to which atoms affected by Langevin dynamics will be adjusted. This temperature will be roughly maintained across the affected atoms through the addition of friction and random forces.
   
• Damping coefficient (1/ps) - langevinDamping
   Langevin coupling coefficient to be applied to all atoms (unless langevinHydrogen is off, in which case only non-hydrogen atoms are affected). If not given, a PDB file is used to obtain coefficients for each atom (see langevinFile and langevinCol below).
   
• Apply to hydrogens - langevinHydrogen
  If this parameter is set to off then the Langevin dynamics the hydrogen atoms aren't considered. This parameter has no effect if Langevin coupling coefficients are read from a PDB file.
   
• Parameters - langevinFile
  PDB file to use for the Langevin coupling coefficients for each atom. If this parameter is not specified, then the PDB file specified by coordinates is used.
   
• PDB column with coefficients - langevinCol
  Column of the PDB file to use for the Langevin coupling coefficients for each atom. The coefficients can be read from any floating point column of the PDB file. A value of 0 indicates that the atom will remain unaffected.

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.

• Temperature rescaling frequency - rescaleFreq
  The equilibration feature of NAMD is activated by specifying the number of timesteps between each temperature rescaling. If this value is given, then the rescaleTemp parameter must also be given to specify the target temperature.
   
• Temperature for equilibration (K) - rescaleTemp
  The temperature to which all velocities will be rescaled every rescaleFreq timesteps.

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].

• Temperature coupling - tCouple
  Specifies whether or not temperature coupling is active.
   
• Temperature (K) - tCoupleTemp
  Temperature to which atoms affected by temperature coupling will be adjusted. This temperature will be roughly maintained across the affected atoms through the addition of forces.
   
• Parameters - tCoupleFile
  PDB file to use for the temperature coupling coefficient for each atom. If this parameter is not specified, then the PDB file specified by coordinates is used.
   
• PDB column with coefficients - tCoupleCol
  Column of the PDB file to use for the temperature coupling coefficient for each atom. This value can be read from any floating point column of the PDB file. A value of 0 indicates that the atom will remain unaffected.

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.

• Temperature reassignment frequency - reassingFreq
  The equilibration feature of NAMD is activated by specifying the number of timesteps between each temperature reassignment. If this value is given, then the reassignTemp parameter must also be given to specify the target temperature.
   
• Temperature for equilibration (K) - reassignTemp
  The temperature to which all velocities will be reassigned every reassignFreq timesteps. This parameter is valid only if reassignFreq has been set.
   
• Temperature increment - reassignIncr
  In order to allow simulated annealing or other slow heating/cooling protocols, reassignIncr will be added to reassignTemp after each reassignment (reassignment is carried out at the first timestep). The reassignHold parameter may be set to limit the final temperature. This parameter is valid only if reassignFreq has been set.
   
• Holding temperature - reassignHold
   The final temperature for reassignment when reassignIncr is set; reassignTemp will be held at this value once it has been reached. This parameter is valid only if reassignIncr has been set.

8.3.13 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.

• First initial step for line minimizer - minTinyStep
  If your minimization is immediately unstable, make this smaller.
   
• Max. initial step for line minimizer - minBabyStep
  If your minimization becomes unstable later, make this smaller.
   
• Gradien reduction factor - minlLineGoal
  Varying this might improve conjugate gradient performance.

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.

• Max. atom move (Å) - maximumMove
  Maximum distance that an atom can move during any single timestep of minimization. This is to insure that atoms do not go flying off into space during the first few timesteps when the largest energy conflicts are resolved.

8.3.14 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.

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.