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Subsections

## Non-bonded interactions

NAMD has a number of options that control the way that non-bonded interactions are calculated. These options are interrelated and can be quite confusing, so this section attempts to explain the behavior of the non-bonded interactions and how to use these parameters.

### Van der Waals interactions

The simplest non-bonded interaction is the van der Waals interaction. In NAMD, van der Waals interactions are always truncated at the cutoff distance, specified by cutoff. The main option that effects van der Waals interactions is the switching parameter. With this option set to on, a smooth switching function will be used to truncate the van der Waals potential energy smoothly at the cutoff distance. A graph of the van der Waals potential with this switching function is shown in Figure 1. If switching is set to off, the van der Waals energy is just abruptly truncated at the cutoff distance, so that energy may not be conserved.

The switching function used is based on the X-PLOR switching function. The parameter switchdist specifies the distance at which the switching function should start taking effect to bring the van der Waals potential to 0 smoothly at the cutoff distance. Thus, the value of switchdist must always be less than that of cutoff.

### Electrostatic interactions

The handling of electrostatics is slightly more complicated due to the incorporation of multiple timestepping for full electrostatic interactions. There are two cases to consider, one where full electrostatics is employed and the other where electrostatics are truncated at a given distance.

First let us consider the latter case, where electrostatics are truncated at the cutoff distance. Using this scheme, all electrostatic interactions beyond a specified distance are ignored, or assumed to be zero. If switching is set to on, rather than having a discontinuity in the potential at the cutoff distance, a shifting function is applied to the electrostatic potential as shown in Figure 2. As this figure shows, the shifting function shifts the entire potential curve so that the curve intersects the x-axis at the cutoff distance. This shifting function is based on the shifting function used by X-PLOR.

Next, consider the case where full electrostatics are calculated. In this case, the electrostatic interactions are not truncated at any distance. In this scheme, the cutoff parameter has a slightly different meaning for the electrostatic interactions -- it represents the local interaction distance, or distance within which electrostatic pairs will be directly calculated every timestep. Outside of this distance, interactions will be calculated only periodically. These forces will be applied using a multiple timestep integration scheme as described in Section 6.3.4.

### Non-bonded force field parameters

• cutoff local interaction distance common to both electrostatic and van der Waals calculations (Å)
Acceptable Values: positive decimal

• switching use switching function?
Acceptable Values: on or off
Default Value: on
Description: If switching is specified to be off, then a truncated cutoff is performed. If switching is turned on, then smoothing functions are applied to both the electrostatics and van der Waals forces. For a complete description of the non-bonded force parameters see Section 5.2. If switching is set to on, then switchdist must also be defined.

• switchdist distance at which to activate switching/splitting function for electrostatic and van der Waals calculations (Å)
Acceptable Values: positive decimal cutoff
Description: Distance at which the switching function should begin to take effect. This parameter only has meaning if switching is set to on. The value of switchdist must be less than or equal to the value of cutoff, since the switching function is only applied on the range from switchdist to cutoff. For a complete description of the non-bonded force parameters see Section 5.2.

• exclude exclusion policy to use
Acceptable Values: none, 1-2, 1-3, 1-4, or scaled1-4
Description: 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.

• dielectric dielectric constant for system
Acceptable Values: decimal 1.0
Default Value: 1.0
Description: 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.

• nonbondedScaling scaling factor for nonbonded forces
Acceptable Values: decimal 0.0
Default Value: 1.0
Description: 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 nonbonded forces acting in the system.

• 1-4scaling scaling factor for 1-4 interactions
Acceptable Values: 0 decimal 1
Default Value: 1.0
Description: Scaling factor for 1-4 interactions. This factor is only used when the 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.

• vdwGeometricSigma use geometric mean to combine L-J sigmas
Acceptable Values: yes or no
Default Value: no
Description: Use geometric mean, as required by OPLS, rather than traditional arithmetic mean when combining Lennard-Jones sigma parameters for different atom types.

• limitdist maximum distance between pairs for limiting interaction strength(Å)
Acceptable Values: non-negative decimal
Default Value: 0.
Description: 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 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; 1.3Å appears to satisfy this for typical simulations but the user is encouraged to experiment. There should be no performance impact from enabling this feature.

• LJcorrection Apply long-range corrections to the system energy and virial to account for neglected vdW forces?
Acceptable Values: yes or no
Default Value: no
Description: Apply an analytical correction to the reported vdW energy and virial that is equal to the amount lost due to switching and cutoff of the LJ potential. The correction will use the average of vdW parameters for all particles in the system and assume a constant, homogeneous distribution of particles beyond the switching distance. See [39] for details (the equations used in the NAMD implementation are slightly different due to the use of a different switching function). Periodic boundary conditions are required to make use of tail corrections.

### PME parameters

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 Use particle mesh Ewald for electrostatics?
Acceptable Values: yes or no
Default Value: no
Description: Turns on particle mesh Ewald.

• PMETolerance PME direct space tolerance
Acceptable Values: positive decimal
Default Value:
Description: Affects the value of the Ewald coefficient and the overall accuracy of the results.

• PMEInterpOrder PME interpolation order
Acceptable Values: positive integer
Default Value: 4 (cubic)
Description: 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.

• PMEGridSpacing maximum space between grid points
Acceptable Values: positive real
Description: 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).

• PMEGridSizeX number of grid points in x dimension
Acceptable Values: positive integer
Description: The grid size partially determines the accuracy and efficiency of PME. For speed, PMEGridSizeX should have only small integer factors (2, 3 and 5).

• PMEGridSizeY number of grid points in y dimension
Acceptable Values: positive integer
Description: The grid size partially determines the accuracy and efficiency of PME. For speed, PMEGridSizeY should have only small integer factors (2, 3 and 5).

• PMEGridSizeZ number of grid points in z dimension
Acceptable Values: positive integer
Description: The grid size partially determines the accuracy and efficiency of PME. For speed, PMEGridSizeZ should have only small integer factors (2, 3 and 5).

• PMEProcessors processors for FFT and reciprocal sum
Acceptable Values: positive integer
Default Value: larger of x and y grid sizes up to all available processors
Description: 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.

• FFTWEstimate Use estimates to optimize FFT?
Acceptable Values: yes or no
Default Value: no
Description: Do not optimize FFT based on measurements, but on FFTW rules of thumb. This reduces startup time, but may affect performance.

• FFTWUseWisdom Use FFTW wisdom archive file?
Acceptable Values: yes or no
Default Value: yes
Description: 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.

• FFTWWisdomFile name of file for FFTW wisdom archive
Acceptable Values: file name
Default Value: FFTW_NAMD_version_platform.txt
Description: 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.

### Full direct parameters

The direct computation of electrostatics is not intended to be used during real calculations, but rather as a testing or comparison measure. Because of the computational complexity for performing direct calculations, this is much slower than using DPMTA or PME to compute full electrostatics for large systems. In the case of periodic boundary conditions, the nearest image convention is used rather than a full Ewald sum.

• FullDirect calculate full electrostatics directly?
Acceptable Values: yes or no
Default Value: no
Description: Specifies whether or not direct computation of full electrostatics should be performed.

### DPME parameters

DPME is an implementation of PME that is no longer included in the released NAMD binaries. We recommend that you use the current PME implementation.

• useDPME Use old DPME code?
Acceptable Values: yes or no
Default Value: no
Description: Switches to old DPME implementation of particle mesh Ewald. The new code is faster and allows non-orthogonal cells so you probably just want to leave this option turned off. If you set cellOrigin to something other than the energy may differ slightly between the old and new implementations. DPME is no longer included in released binaries.

### DPMTA parameters

DPMTA is no longer included in the released NAMD binaries. We recommend that you instead use PME with a periodic system because it conserves energy better, is more efficient, and is better parallelized. If you must have the fast multipole algorithm you may compile NAMD yourself.

These parameters control the options to DPMTA, an algorithm used to provide full electrostatic interactions. DPMTA is a modified version of the FMA (Fast Multipole Algorithm) and, unfortunately, most of the parameters still refer to FMA rather than DPMTA for historical reasons. Don't be confused!

For a further description of how exactly full electrostatics are incorporated into NAMD, see Section 6.3.4. For a greater level of detail about DPMTA and the specific meaning of its options, see the DPMTA distribution which is available via anonymous FTP from the site ftp.ee.duke.edu in the directory /pub/SciComp/src.

• FMA use full electrostatics?
Acceptable Values: on or off
Default Value: off
Description: Specifies whether or not the DPMTA algorithm from Duke University should be used to compute the full electrostatic interactions. If set to on, DPMTA will be used with a multiple timestep integration scheme to provide full electrostatic interactions as detailed in Section 6.3.4. DPMTA is no longer included in released binaries.

• FMALevels number of levels to use in multipole expansion
Acceptable Values: positive integer
Default Value: 5
Description: Number of levels to use for the multipole expansion. This parameter is only used if FMA is set to on. A value of 4 should be sufficient for systems with less than 10,000 atoms. A value of 5 or greater should be used for larger systems.

• FMAMp number of multipole terms to use for FMA
Acceptable Values: positive integer
Default Value: 8
Description: Number of terms to use in the multipole expansion. This parameter is only used if FMA is set to on. If the FMAFFT is set to on, then this value must be a multiple of 4. The default value of 8 should be suitable for most applications.

• FMAFFT use DPMTA FFT enhancement?
Acceptable Values: on or off
Default Value: on
Description: Specifies whether or not the DPMTA code should use the FFT enhancement feature. This parameter is only used if FMA is set to on. If FMAFFT is set to on, the value of FMAMp must be set to a multiple of 4. This feature offers substantial benefits only for values of FMAMp of 8 or greater. This feature will substantially increase the amount of memory used by DPMTA.

• FMAtheta DPMTA theta parameter (radians)
Acceptable Values: decimal
Default Value: 0.715
Description: This parameter specifies the value of the theta parameter used in the DPMTA calculation. The default value is based on recommendations by the developers of the code.

• FMAFFTBlock blocking factor for FMA FFT
Acceptable Values: positive integer
Default Value: 4
Description: The blocking factor for the FFT enhancement to DPMTA. This parameter is only used if both FMA and FMAFFT are set to on. The default value of 4 should be suitable for most applications.

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