We report major algorithmic improvements of the UNRES package for physics-based coarse-grained simulations of proteins. These include (i) introduction of interaction lists to optimize computations, (ii) transforming the inertia matrix to a pentadiagonal form to reduce computing and memory requirements, (iii) removing explicit angles and dihedral angles from energy expressions and recoding the most time-consuming energy/force terms to minimize the number of operations and to improve numerical stability, (iv) using OpenMP to parallelize those sections of the code for which distributed-memory parallelization involves unfavorable computing/communication time ratio, and (v) careful memory management to minimize simultaneous access of distant memory sections. The new code enables us to run molecular dynamics simulations of protein systems with size exceeding 100,000 amino-acid residues, reaching over 1 ns/day (1 μs/day in all-atom timescale) with 24 cores for proteins of this size. Parallel performance of the code and comparison of its performance with that of AMBER, GROMACS and MARTINI 3 is presented. 相似文献
We describe the development of a coarse‐grained (CG) force field for nylon‐6 (polycaprolactam) and its application to the simulation of the structure and macromolecular dynamics within cylindrical fibres formed by this polymer, having diameters in the 14–28 nm range. Our CG model is based on the MARTINI force field for the non‐bonded interactions and on Boltzmann‐inverted gas‐phase atomistic simulations for intramolecular stretching and bending energies. The simulations are carried out on infinite, isolated nanofibres at temperatures of 300, 400 and 500 K, with different starting configurations. Starting from ordered chain‐extended configurations, we simulate the melting of the polymer in the nanofibres and, after cooling back to room temperature, its re‐crystallization in a chain‐folded lamellar configuration. This agrees with experimental observations on electrospun nylon‐6 nanofibres and demonstrated the suitability of the approach for the simulation of these systems. The effect of nanoscale confinement on the structure and dynamics of the polymer chains is extensively discussed.
IBIsCO is a parallel molecular dynamics simulation package developed specially for coarse-grained simulations with numerical potentials derived by the iterative Boltzmann inversion (IBI) method (Reith et al., J Comput Chem 2003, 24, 1624). In addition to common features of molecular dynamics programs, the techniques of dissipative particle dynamics (Groot and Warren, J Chem Phys 1997, 107, 4423) and Lowe-Andersen dynamics (Lowe, Europhys Lett 1999, 47, 145) are implemented, which can be used both as thermostats and as sources of friction to compensate the loss of degrees of freedom by coarse-graining. The reverse nonequilibrium molecular dynamics simulation method (Müller-Plathe, Phys Rev E 1999, 59, 4894) for the calculation of viscosities is also implemented. Details of the algorithms, functionalities, implementation, user interfaces, and file formats are described. The code is parallelized using PE_MPI on PowerPC architecture. The execution time scales satisfactorily with the number of processors. 相似文献
In this study, dissipative particle dynamics is employed to investigate the complexation of poly(amido amine) dendrimer and single‐stranded DNA (ssDNA). A coarse‐grained model for ssDNA is constructed, which reproduces correctly the conformational behavior of the ssDNA molecules. The effects of pH, dendrimer generation, ionic strength, and dendrimer/ssDNA charge ratio on DNA–dendrimer complexes are explored. Simulation results show that ssDNA molecules can be significantly condensed by dendrimers and stable complexes are obtained by regulating the pH value. The ssDNA chain penetration would complicate its release from dendrimer, while this can be tuned by different generations of dendrimer. Salt concentration affects the size and stability of the complexes through ion screening effect. Dendrimer/ssDNA charge ratio can be used to control the size and morphology of the complex. This work can help design dendrimer‐based gene vectors. 相似文献
Bottom‐up prediction of physical performance of glass‐forming (GF) polymers via coarse‐grained (CG) modeling is challenging because these CG models normally experience significantly altered dynamics that strongly vary with temperature. Building upon the recently developed energy‐renormalization (ER) coarse‐graining method based on molecular dynamics simulations, generalized entropy theory (GET) is employed to theoretically investigate the influence of fundamental molecular parameters on CG modeling of polymers having different glass “fragilities” Taking a linear polymer melt as a model system within the GET framework, it is shown that the chain bending rigidity and cohesive interaction play critical roles in the glass formation of polymers and their CG analogs. To coarse‐grain polymers having a higher fragility index, it requires greater magnitudes of ER factor εCG to rescale the cohesive interaction strength under coarse‐graining and thus recover the atomistic relaxation dynamics over a wide temperature range. The GET further predicts that a higher degree of coarse‐graining generally requires greater magnitudes of εCG due to the influence of loss of configuration entropy sc on the dynamics. GET analyses herein theoretically demonstrate the efficacy of the ER method toward building a multiscale temperature transferable modeling framework for GF polymers, and confirm the importance of preserving sc in CG modeling of dynamics of soft materials. 相似文献
In this work, the combined iterative Boltzmann inversion/conditional reversible work scheme is extended with a little modifications to derive the systematically coarse‐grained (CG) potentials for simulating two typical atactic polymer blends composed of poly(methyl methacrylate) (PMMA) and poly(vinyl chloride) (PVC) or polystyrene (PS). Molecular dynamics simulations are extensively performed on the two blends with a wide formulation range. It is revealed by these simulations that, throughout the entire composition range, the PMMA/PVC blend is homogeneous whereas the PMMA/PS blend undergoes phase separation, which agrees well with the experimental observation that the former exhibits strong interactions that are absent in the latter. Depending upon the formulation, the immiscible PMMA/PS blend presents one single‐ or double‐continuous phase. It is further confirmed that intermolecular interactions play the key roles in forming the phase morphologies, which in turn can be inferred from only the three nonbonded CG potentials of one unlike pair and two like pairs.
The coarse-grained structural model such as Gaussian network has played a vital role in the normal mode studies for understanding protein dynamics related to biological functions. However, for the large proteins, the Gaussian network model is computationally unfavorable for diagonalization of Hessian (stiffness) matrix for the normal mode studies. In this article, we provide the coarse-graining method, referred to as \"dynamic model condensation,\" which enables the further coarse-graining of protein structures consisting of small number of residues. It is shown that the coarser-grained structures reconstructed by dynamic model condensation exhibit the dynamic characteristics, such as low-frequency normal modes, qualitatively comparable to original structures. This sheds light on that dynamic model condensation and may enable one to study the large protein dynamics for gaining insight into biological functions of proteins. 相似文献
We have recently developed a new singularity‐free algorithm for Brownian dynamics simulation of free rotational diffusion. The algorithm is rigorously derived from kinetic theory and makes use of the Cartesian components of the rotation vector as the generalized coordinates describing angular orientation. Here, we report on the application of this new algorithm in Brownian dynamics simulations of transient electro‐optical properties. This work serves two main purposes. Firstly, it demonstrates the integrity of the new algorithm for BD‐simulations of the most common transient electro‐optic experiments. Secondly, it provides new insight into the performance of the new algorithm compared to algorithms that make use of the Euler angles. We study the transient electrically induced birefringence in dilute solutions of rigid particles with anisotropic polarization tensor in response to external electric field pulses. The use of both one single electric pulse and two electric pulses with opposite polarity are being analyzed. We document that the new singularity‐free algorithm performs flawlessly. We find that, for these types of systems, the new singularity‐free algorithm, in general, outperforms similar algorithms based on the Euler angles. In a wider perspective, the most important aspect of this work is that it serves as an important reference for future development of efficient BD‐algorithms for studies of more complex systems. These systems include polymers consisting of rigid segments with single‐segment translational–rotational coupling, segment–segment fluid‐dynamic interactions and holonomic constraints.
A goal across multiple scientific fields (e.g. separations, polymer processing, and biomaterials) is to understand polymer dynamics at solid/liquid interfaces. In the last two decades, rapid developments in single-molecule techniques have revolutionized our ability to directly observe molecular behaviors with ultra-high spatial/temporal resolution and to decouple the elementary processes that were often veiled in ensemble experiments. This review provided an overview of principle and realization of two single-molecule fluorescence techniques that were often used to study the interfacial dynamics. In addition, this review updated recent progress in the discovery and understanding of dynamical anomalies of polymers at solid/liquid interfaces using these single-molecule techniques, emphasizing important elementary processes of diffusion, adsorption, and desorption. 相似文献
An updated mesoscopic model for transient forces between two star polymers is presented. Calculation of the transient forces is based on the response of a vectorial structure parameter between two star polymers and differs from previous models that used a scalar structure parameter. The update of the model is motivated by the occurrence of two distinct processes in previous small‐scale simulations of two star polymers moving past each other. A simple model that takes these processes into account turns out to fit into an obvious generalization of the RaPiD model introduced by us some time ago. The model reproduces forces from the simulation quite well, and at the same time removes an unphysical feature of the RaPiD model used so far. 相似文献
