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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.

Figure 1: Graph of van der Waals potential with and without the application of the switching function. With the switching function active, the potential is smoothly reduced to 0 at the cutoff distance. Without the switching function, there is a discontinuity where the potential is truncated.
\includegraphics{figures/switching}

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.

Figure 2: Graph showing an electrostatic potential with and without the application of the shifting function.
\includegraphics{figures/shifting}

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.

Figure 3: Graph showing an electrostatic potential when full electrostatics are used within NAMD, with one curve portion calculated directly and the other calculated using DPMTA.
\includegraphics{figures/fmaOn}

Non-bonded force field parameters

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.

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 $ {\mathcal O}(N^2)$ 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.

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.

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.


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Next: Water Models Up: Force Field Parameters Previous: Potential energy functions   Contents   Index
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