5 research outputs found
TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD
Molecular
dynamics (MD) simulation engines use a variety of different
approaches for modeling molecular systems with force fields that govern
their dynamics and describe their topology. These different approaches
introduce incompatibilities between engines, and previously published
software bridges the gaps between many popular MD packages, such as
between CHARMM and AMBER or GROMACS and LAMMPS. While there are many
structure building tools available that generate topologies and structures
in CHARMM format, only recently have mechanisms been developed to
convert their results into GROMACS input. We present an approach to
convert CHARMM-formatted topology and parameters into a format suitable
for simulation with GROMACS by expanding the functionality of TopoTools,
a plugin integrated within the widely used molecular visualization
and analysis software VMD. The conversion process was diligently tested
on a comprehensive set of biological molecules <i>in vacuo</i>. The resulting comparison between energy terms shows that the translation
performed was lossless as the energies were unchanged for identical
starting configurations. By applying the conversion process to conventional
benchmark systems that mimic typical modestly sized MD systems, we
explore the effect of the implementation choices made in CHARMM, NAMD,
and GROMACS. The newly available automatic conversion capability breaks
down barriers between simulation tools and user communities and allows
users to easily compare simulation programs and leverage their unique
features without the tedium of constructing a topology twice
Reconsidering Dispersion Potentials: Reduced Cutoffs in Mesh-Based Ewald Solvers Can Be Faster Than Truncation
Long-range dispersion interactions
have a critical influence on
physical quantities in simulations of inhomogeneous systems. However,
the perceived computational overhead of long-range solvers has until
recently discouraged their implementation in molecular dynamics packages.
Here, we demonstrate that reducing the cutoff radius for local interactions
in the recently introduced particle–particle particle−mesh
(PPPM) method for dispersion [Isele-Holder et al., <i>J. Chem.
Phys.</i>, <b>2012</b>, <i>137</i>, 174107] can
actually often be faster than truncating dispersion interactions.
In addition, because all long-range dispersion interactions are incorporated,
physical inaccuracies that arise from truncating the potential can
be avoided. Simulations using PPPM or other mesh Ewald solvers for
dispersion can provide results more accurately and more efficiently
than simulations that truncate dispersion interactions. The use of
mesh-based approaches for dispersion is now a viable alternative for
all simulations containing dispersion interactions and not merely
those where inhomogeneities were motivating factors for their use.
We provide a set of parameters for the dispersion PPPM method using
either <i>i</i><b>k</b> or analytic differentiation
that we recommend for future use and demonstrate increased simulation
efficiency by using the long-range dispersion solver in a series of
performance tests on massively parallel computers
Reconsidering Dispersion Potentials: Reduced Cutoffs in Mesh-Based Ewald Solvers Can Be Faster Than Truncation
Long-range dispersion interactions
have a critical influence on
physical quantities in simulations of inhomogeneous systems. However,
the perceived computational overhead of long-range solvers has until
recently discouraged their implementation in molecular dynamics packages.
Here, we demonstrate that reducing the cutoff radius for local interactions
in the recently introduced particle–particle particle−mesh
(PPPM) method for dispersion [Isele-Holder et al., <i>J. Chem.
Phys.</i>, <b>2012</b>, <i>137</i>, 174107] can
actually often be faster than truncating dispersion interactions.
In addition, because all long-range dispersion interactions are incorporated,
physical inaccuracies that arise from truncating the potential can
be avoided. Simulations using PPPM or other mesh Ewald solvers for
dispersion can provide results more accurately and more efficiently
than simulations that truncate dispersion interactions. The use of
mesh-based approaches for dispersion is now a viable alternative for
all simulations containing dispersion interactions and not merely
those where inhomogeneities were motivating factors for their use.
We provide a set of parameters for the dispersion PPPM method using
either <i>i</i><b>k</b> or analytic differentiation
that we recommend for future use and demonstrate increased simulation
efficiency by using the long-range dispersion solver in a series of
performance tests on massively parallel computers
Reconsidering Dispersion Potentials: Reduced Cutoffs in Mesh-Based Ewald Solvers Can Be Faster Than Truncation
Long-range dispersion interactions
have a critical influence on
physical quantities in simulations of inhomogeneous systems. However,
the perceived computational overhead of long-range solvers has until
recently discouraged their implementation in molecular dynamics packages.
Here, we demonstrate that reducing the cutoff radius for local interactions
in the recently introduced particle–particle particle−mesh
(PPPM) method for dispersion [Isele-Holder et al., <i>J. Chem.
Phys.</i>, <b>2012</b>, <i>137</i>, 174107] can
actually often be faster than truncating dispersion interactions.
In addition, because all long-range dispersion interactions are incorporated,
physical inaccuracies that arise from truncating the potential can
be avoided. Simulations using PPPM or other mesh Ewald solvers for
dispersion can provide results more accurately and more efficiently
than simulations that truncate dispersion interactions. The use of
mesh-based approaches for dispersion is now a viable alternative for
all simulations containing dispersion interactions and not merely
those where inhomogeneities were motivating factors for their use.
We provide a set of parameters for the dispersion PPPM method using
either <i>i</i><b>k</b> or analytic differentiation
that we recommend for future use and demonstrate increased simulation
efficiency by using the long-range dispersion solver in a series of
performance tests on massively parallel computers
Micellization Studied by GPU-Accelerated Coarse-Grained Molecular Dynamics
The computational design of advanced materials based on surfactant self-assembly without ever stepping foot in the laboratory is an important goal, but there are significant barriers to this approach, because of the limited spatial and temporal scales accessible by computer simulations. In this paper, we report our work to bridge the gap between laboratory and computational time scales by implementing the coarse-grained (CG) force field previously reported by Shinoda et al. [Shinoda, W.; DeVane, R.; Klein, M. L. <i>Mol. Simul</i>. <b>2007</b>, <i>33</i>, 27–36] into the HOOMD-Blue graphical processing unit (GPU)-accelerated molecular dynamics (MD) software package previously reported by Anderson et al. [Anderson, J. A.; Lorenz, C. D.; Travesset, A. <i>J. Comput. Phys</i>. <b>2008</b>, <i>227</i>, 5342–5359]. For a system of 25 750 particles, this implementation provides performance on a single GPU, which is superior to that of a widely used parallel MD simulation code running on an optimally sized CPU-based cluster. Using our GPU setup, we have collected 0.6 ms of MD trajectory data for aqueous solutions of 7 different nonionic polyethylene glycol (PEG) surfactants, with most of the systems studied representing ∼1 000 000 atoms. From this data, we calculated various properties as a function of the length of the hydrophobic tails and PEG head groups. Specifically, we determined critical micelle concentrations (CMCs), which are in good agreement with experimental data, and characterized the size and shape of micelles. However, even with the microsecond trajectories employed in this study, we observed that the micelles composed of relatively hydrophobic surfactants are continuing to grow at the end of our simulations. This suggests that the final micelle size distributions of these systems are strongly dependent on initial conditions and that either longer simulations or advanced sampling techniques are needed to properly sample their equilibrium distributions. Nonetheless, the combination of coarse-grained modeling and GPU acceleration marks a significant step toward the computational prediction of the thermodynamic properties of slowly evolving surfactant systems