Interdisciplinary Applied Mathematics

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16.1.6 MD Software


A number    of    MD    programs are    available    on    the    Web    for    free    download.


Some of the MD programs that are popularly used by the computational


chemistry and biology community are listed in Table 16.3.

16.2 MD-Continuum Coupling


MD simulations can be employed only for a short time and very small length scales due to their large computational requirements compared to the computational complexity of continuum discretizations. Multiscale approaches both in time and space can overcome this difficulty. The coupling of MD to Navier-Stokes equations would extend the range of applicability of both approaches and provide a unifying description of liquid flows from nanoscales to larger scales. The incompressible Navier-Stokes equations are involved in the coupling, although some authors have attempted to couple MD to compressible Navier-Stokes equations; see, for example, (Flekkoy et    al.,    2000).    In    the    following    we    will    present    the    main ideas of


four different coupling strategies:
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TABLE 16.3. A list of some commonly used MD packages.


MD Package


Website


GROMACS


http://www.gromacs. org


AMBER


http://amber.scripps.edu/


CHARMM


http://yuri. harvard, edu/


NAMD


http: //www. ks.uiuc.edu/Research/narnd/


Chemical


http://www.uku.fi/ thassine/chemical/


Insight II


http://www. accelrys. сот/insight/


ORAC


http://www. chim.unifi.it:8080/orac

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Bin# 3 Bin # 2 Bin # 1


Bin # 0


Wall


FIGURE 16.3. Domain for MD-Continuum coupling.


structure in the fluid at interfaces and especially for density (Koplik and Banavar, 1995). The two-domain coupling would therefore have the form shown in the sketch of Figure 16.3, consisting of a region (MD) where the molecular dynamics simulation is performed, the region where the Navier-Stokes equations will be solved, and an overlap region, where both descriptions are valid. However, in order to terminate the MD region, in addition to standard particle motion in the overlap region a constraint should be imposed of the form

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