New faster CHARMM molecular dynamics engine

We introduce a new faster molecular dynamics (MD) engine into the CHARMM software package. The new MD engine is faster both in serial (i.e., single CPU core) and parallel execution. Serial performance is approximately two times higher than in the previous version of CHARMM. The newly programmed parallelization method allows the MD engine to parallelize up to hundreds of CPU cores. © 2013 Wiley Periodicals, Inc.     

MPI/OpenMP hybrid parallel implementation of second-order M?ller�CPlesset perturbation theory using numerical quadratures

An algorithm for massively parallel computers is developed for energy calculations of second-order M?ller?CPlesset (MP2) perturbation theory with numerical quadratures. Message Passing Interface (MPI) and Open Multi-Processing (OpenMP) technologies are utilized for inter-node and intra-node parallelization, respectively. Computational tasks and intermediates are distributed across nodes by dividing quadrature points, and the distributed data are stored in memory. Benchmark calculations were performed on 256?C8,192 CPU cores, and we observed the speed-ups 4,534?C6,266 for 8,192 cores. A large calculation for fullerene (C₆₀) with aug-cc-pCVTZ (3,540 basis functions) was completed in ca. 4.8?h on 8,192 cores without invoking molecular symmetry.     

GPU accelerated implementation of NCI calculations using promolecular density

The NCI approach is a modern tool to reveal chemical noncovalent interactions. It is particularly attractive to describe ligand–protein binding. A custom implementation for NCI using promolecular density is presented. It is designed to leverage the computational power of NVIDIA graphics processing unit (GPU) accelerators through the CUDA programming model. The code performances of three versions are examined on a test set of 144 systems. NCI calculations are particularly well suited to the GPU architecture, which reduces drastically the computational time. On a single compute node, the dual‐GPU version leads to a 39‐fold improvement for the biggest instance compared to the optimal OpenMP parallel run (C code, icc compiler) with 16 CPU cores. Energy consumption measurements carried out on both CPU and GPU NCI tests show that the GPU approach provides substantial energy savings. © 2017 Wiley Periodicals, Inc.     

Hybrid MPI/OpenMP parallelization of the effective fragment potential method in the libefp software library

A new hybrid MPI/OpenMP parallelization scheme is introduced for the Effective Fragment Potential (EFP) method implemented in the libefp software library. The new implementation employs dynamic load balancing algorithm that uses a master/slave model. The software shows excellent parallel scaling up to several hundreds of CPU‐cores across multiple nodes. The code uses functions only from the well‐established MPI‐1 standard that simplifies portability of the library. This new parallel EFP implementation greatly expands the applicability of the EFP and QM/EFP methods by extending attainable time‐ and length‐scales. © 2014 Wiley Periodicals, Inc.     

Massively parallel implementation of 3D‐RISM calculation with volumetric 3D‐FFT

A new three‐dimensional reference interaction site model (3D‐RISM) program for massively parallel machines combined with the volumetric 3D fast Fourier transform (3D‐FFT) was developed, and tested on the RIKEN K supercomputer. The ordinary parallel 3D‐RISM program has a limitation on the number of parallelizations because of the limitations of the slab‐type 3D‐FFT. The volumetric 3D‐FFT relieves this limitation drastically. We tested the 3D‐RISM calculation on the large and fine calculation cell (2048³ grid points) on 16,384 nodes, each having eight CPU cores. The new 3D‐RISM program achieved excellent scalability to the parallelization, running on the RIKEN K supercomputer. As a benchmark application, we employed the program, combined with molecular dynamics simulation, to analyze the oligomerization process of chymotrypsin Inhibitor 2 mutant. The results demonstrate that the massive parallel 3D‐RISM program is effective to analyze the hydration properties of the large biomolecular systems. © 2014 Wiley Periodicals, Inc.     

Message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines

A mixed parallel scheme that combines message passing interface (MPI) and multithreading was implemented in the AutoDock Vina molecular docking program. The resulting program, named VinaLC, was tested on the petascale high performance computing (HPC) machines at Lawrence Livermore National Laboratory. To exploit the typical cluster‐type supercomputers, thousands of docking calculations were dispatched by the master process to run simultaneously on thousands of slave processes, where each docking calculation takes one slave process on one node, and within the node each docking calculation runs via multithreading on multiple CPU cores and shared memory. Input and output of the program and the data handling within the program were carefully designed to deal with large databases and ultimately achieve HPC on a large number of CPU cores. Parallel performance analysis of the VinaLC program shows that the code scales up to more than 15K CPUs with a very low overhead cost of 3.94%. One million flexible compound docking calculations took only 1.4 h to finish on about 15K CPUs. The docking accuracy of VinaLC has been validated against the DUD data set by the re‐docking of X‐ray ligands and an enrichment study, 64.4% of the top scoring poses have RMSD values under 2.0 Å. The program has been demonstrated to have good enrichment performance on 70% of the targets in the DUD data set. An analysis of the enrichment factors calculated at various percentages of the screening database indicates VinaLC has very good early recovery of actives. © 2013 Wiley Periodicals, Inc.     

Performance of heterogeneous computing with graphics processing unit and many integrated core for hartree potential calculations on a numerical grid

We investigated the performance of heterogeneous computing with graphics processing units (GPUs) and many integrated core (MIC) with 20 CPU cores (20×CPU). As a practical example toward large scale electronic structure calculations using grid‐based methods, we evaluated the Hartree potentials of silver nanoparticles with various sizes (3.1, 3.7, 4.9, 6.1, and 6.9 nm) via a direct integral method supported by the sinc basis set. The so‐called work stealing scheduler was used for efficient heterogeneous computing via the balanced dynamic distribution of workloads between all processors on a given architecture without any prior information on their individual performances. 20×CPU + 1GPU was up to ～1.5 and ～3.1 times faster than 1GPU and 20×CPU, respectively. 20×CPU + 2GPU was ～4.3 times faster than 20×CPU. The performance enhancement by CPU + MIC was considerably lower than expected because of the large initialization overhead of MIC, although its theoretical performance is similar with that of CPU + GPU. © 2016 Wiley Periodicals, Inc.     

分子动力学模拟计算在通用图形处理芯片上的实现

将在计算生物分子中广泛应用的CHARMM力场应用于Windows computer cluster server(WCCS)环境下, 并实现了该力场及分子动力学模拟程序的通用显卡(GPU)并行计算. 对一些多肽链的动力学模拟结果显示, 与CPU计算相比, GPU计算在计算速度上有巨大的提升. 与64位Athlon 2.0G相比, 在NVIDIA GeForce 8800 GT显卡上的动力学模拟速度提高了至少10倍, 而且这个效率比会随着模拟体系及每块尺寸的增大而增大. 模拟体系的增大使得GPU并行单元的计算空载相对减少, 块尺寸的增大使缓存区尺寸相对减少, 单块计算效率得以提高. 在测试样本中, 该效率比最高可达到28倍以上. 利用GPU计算还对一条含有397个原子的多肽链进行了分子动力学模拟, 给出了氢键分布随时间的变化结果.     

New parallel algorithm for MP2 energy gradient calculations

A new parallel algorithm has been developed for calculating the analytic energy derivatives of full accuracy second order Møller‐Plesset perturbation theory (MP2). Its main projected application is the optimization of geometries of large molecules, in which noncovalent interactions play a significant role. The algorithm is based on the two‐step MP2 energy calculation algorithm developed recently and implemented into the quantum chemistry program, GAMESS. Timings are presented for test calculations on taxol (C₄₇H₅₁NO₁₄) with the 6‐31G and 6‐31G(d) basis sets (660 and 1032 basis functions, 328 correlated electrons) and luciferin (C₁₁H₈N₂O₃S₂) with aug‐cc‐pVDZ and aug‐cc‐pVTZ (530 and 1198 basis functions, 92 correlated electrons). The taxol 6‐31G(d) calculations are also performed with up to 80 CPU cores. The results demonstrate the high parallel efficiency of the program. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007     

MPI/OpenMP hybrid parallel algorithm for resolution of identity second‐order Møller–Plesset perturbation calculation of analytical energy gradient for massively parallel multicore supercomputers

A massively parallel algorithm of the analytical energy gradient calculations based the resolution of identity Møller–Plesset perturbation (RI‐MP2) method from the restricted Hartree–Fock reference is presented for geometry optimization calculations and one‐electron property calculations of large molecules. This algorithm is designed for massively parallel computation on multicore supercomputers applying the Message Passing Interface (MPI) and Open Multi‐Processing (OpenMP) hybrid parallel programming model. In this algorithm, the two‐dimensional hierarchical MP2 parallelization scheme is applied using a huge number of MPI processes (more than 1000 MPI processes) for acceleration of the computationally demanding O (N ⁵) step such as calculations of occupied–occupied and virtual–virtual blocks of MP2 one‐particle density matrix and MP2 two‐particle density matrices. The new parallel algorithm performance is assessed using test calculations of several large molecules such as buckycatcher C₆₀@C₆₀H₂₈ (144 atoms, 1820 atomic orbitals (AOs) for def2‐SVP basis set, and 3888 AOs for def2‐TZVP), nanographene dimer (C₉₆H₂₄)₂ (240 atoms, 2928 AOs for def2‐SVP, and 6432 AOs for cc‐pVTZ), and trp‐cage protein 1L2Y (304 atoms and 2906 AOs for def2‐SVP) using up to 32,768 nodes and 262,144 central processing unit (CPU) cores of the K computer. The results of geometry optimization calculations of trp‐cage protein 1L2Y at the RI‐MP2/def2‐SVP level using the 3072 nodes and 24,576 cores of the K computer are presented and discussed to assess the efficiency of the proposed algorithm. © 2017 Wiley Periodicals, Inc.     

Accelerating molecular docking calculations using graphics processing units

The generation of molecular conformations and the evaluation of interaction potentials are common tasks in molecular modeling applications, particularly in protein-ligand or protein-protein docking programs. In this work, we present a GPU-accelerated approach capable of speeding up these tasks considerably. For the evaluation of interaction potentials in the context of rigid protein-protein docking, the GPU-accelerated approach reached speedup factors of up to over 50 compared to an optimized CPU-based implementation. Treating the ligand and donor groups in the protein binding site as flexible, speedup factors of up to 16 can be observed in the evaluation of protein-ligand interaction potentials. Additionally, we introduce a parallel version of our protein-ligand docking algorithm PLANTS that can take advantage of this GPU-accelerated scoring function evaluation. We compared the GPU-accelerated parallel version to the same algorithm running on the CPU and also to the highly optimized sequential CPU-based version. In terms of dependence of the ligand size and the number of rotatable bonds, speedup factors of up to 10 and 7, respectively, can be observed. Finally, a fitness landscape analysis in the context of rigid protein-protein docking was performed. Using a systematic grid-based search methodology, the GPU-accelerated version outperformed the CPU-based version with speedup factors of up to 60.     

Photodissociation of HBr. 1. Electronic structure, photodissociation dynamics, and vector correlation coefficients

Ab initio potential energy curves, transition dipole moments, and spin-orbit coupling matrix elements are computed for HBr. These are then used, within the framework of time-dependent quantum-mechanical wave-packet calculations, to study the photodissociation dynamics of the molecule. Total and partial integral cross sections, the branching fraction for the formation of excited-state bromine atoms Br(2P(1/2)), and the lowest order anisotropy parameters, beta, for both ground and excited-state bromine are calculated as a function of photolysis energy and compared to experimental and theoretical data determined previously. Higher order anisotropy parameters are computed for the first time for HBr and compared to recent experimental measurements. A new expression for the Re[a1(3) (parallel, perpendicular)] parameter describing coherent parallel and perpendicular production of ground-state bromine in terms of the dynamical functions is given. Although good agreement is obtained between the theoretical predictions and the experimental measurements, the discrepancies are analyzed to establish how improvements might be achieved. Insight is obtained into the nonadiabatic dynamics by comparing the results of diabatic and fully adiabatic calculations.     

Vectorization of the general Monte Carlo classical trajectory program VENUS

The general chemical dynamics computer program VENUS is used to perform classical trajectory simulations for large polyatomic systems, with many atoms and complicated potential energy functions. To simulate an ensemble of many trajectories requires a large amount of CPU time. Since each trajectory is independent, it is possible to parallel process a large set of trajectories instead of processing the trajectories by the conventional sequential approach. This enhances the vectorizability of the VENUS program, since the integration of Hamilton's equations of motion and the gradient evaluation, which comprise 97.8% of the CPU, can each be parallel processed. In this article, the vectorization and ensuing optimization of VENUS on the CRAY-YMP and IBM-3090 are presented in terms of both global strategies and technical details. A switching algorithm is designed to enhance the vector performance and to minimize the memory storage. A performance of 140 MFLOPS and a vector/scalar execution rate ratio of 10.6 are observed when this new version of VENUS is used to study the association of CH₃ with the H(Ar)₁₂ cluster on the CRAY-YMP.     

Hydrophobicity, shape, and pi-electron contributions during translesion DNA synthesis

Translesion DNA synthesis, the ability of a DNA polymerase to misinsert a nucleotide opposite a damaged DNA template, represents a common route toward mutagenesis and possibly disease development. To further define the mechanism of this promutagenic process, we synthesized and tested the enzymatic incorporation of two isosteric 5-substituted indolyl-2'deoxyriboside triphosphates opposite an abasic site. The catalytic efficiency for the incorporation of the 5-cyclohexene-indole derivative opposite an abasic site is 75-fold greater than that for the 5-cyclohexyl-indole derivative. The higher efficiency reflects a substantial increase in the k(pol) value (compare 25 versus 0.5 s(-1), respectively) as opposed to an influence on ground-state binding of either non-natural nucleotide. The faster k(pol) value for the 5-cyclohexene-indole derivative indicates that pi-electron density enhances the rate of the enzymatic conformational change step required for insertion opposite the abasic site. However, the kinetic dissociation constants for the non-natural nucleotides are identical and indicate that pi-electron density does not directly influence ground-state binding opposite the DNA lesion. Surprisingly, each non-natural nucleotide can be incorporated opposite natural templating bases, albeit with a greatly reduced catalytic efficiency. In this instance, the lower catalytic efficiency is caused by a substantial decrease in the k(pol) value rather than perturbations in ground-state binding. Collectively, these data indicate that the rate of the conformational change during translesion DNA synthesis depends on pi-electron density, while the enhancement in ground-state binding appears related to the size and shape of the non-natural nucleotide.     

Structural, electronic, and vibrational characterization of Fe-HNO porphyrinates by density functional theory

A recent report of the structural and vibrational properties of heme-bound HNO in myoglobin, MbHNO, revealed a long Fe-N(HNO) bond with the hydrogen atom bonded to the coordinated N atom. The Fe-N(H)-O moiety was reported to exhibit an unusually high Fe-N(HNO) stretching frequency relative to those of the corresponding [FeNO]6 and [FeNO]7 porphyrinates, despite the Fe-N(HNO) bond being longer than either of its Fe-N(NO) counterparts. Herein, we present results from density functional theory calculations of an active site model of MbHNO that support the previous assignment and clarify this seemingly contradictory result. The results are consistent with the experimental evidence for a ground-state Fe-N(H)-O structure having a long Fe-N(HNO) bond and a uniquely high nu(Fe)(-)(N(HNO)) frequency. This high frequency is the result of the correspondingly low reduced mass of the normal mode, which is largely attributable to significant motion of the N-bound hydrogen atom. Additionally, the calculations show the Fe-N(H)O bonding in this complex to be remarkably insensitive to whether the HNO and ImH ligand planes are parallel or perpendicular. This is attributed to insensitivities of the Fe-L(axial) characters of molecular orbitals to the relative HNO and ImH orientation in both the parallel and perpendicular conformers.     

Electronic states of SnS and SnS+: a configuration interaction study

Ab initio based multireference configuration interaction calculations are carried out for SnS and its monopositive ion using effective core potentials. Potential energy curves and spectroscopic constants of the low-lying states of SnS and SnS+ are computed. The ground-state dissociation energies of the neutral and ionic species are about 4.71 and 2.86 eV, respectively which compare well with the available thermochemical data. The effect of d-electron correlation on the spectroscopic constants of a few low-lying states has been studied. The spin-orbit interaction has also been included to investigate its effect on the spectroscopic properties of both SnS and SnS+. Dipole moment and transition moment curves are also constructed as a function of the bond length. Transition probabilities of some dipole-allowed and spin-forbidden transitions are studied. Radiative lifetimes of a few low-lying states are estimated. The E1sigma+-X1sigma+ transition of SnS is predicted to be the strongest one. The components of the A2sigma(+)(1/2)-X2(2)pi(1/2) transition with parallel and perpendicular polarization are separately analyzed. The vertical ionization energies of the ground-state SnS to the ground and low-lying excited states of the monopositive ion are calculated.     

Relativistic all-electron Dirac-Fock-Breit calculations on xenon fluorides (XeFn,n = 1, 2, 4, 6)

The MOLFDIR package of programs is used to perform fully relativistic all-electron Dirac-Fock and Dirac-Fock-Breit calculations for the the XeF_n (n = 1, 2, 4, 6) molecules assuming experimental symmetries. The Xe-F bound length for XeF₂, XeF₄, and XeF₆ is optimized and the total ground-state energies are reported. The variation of the relativistic energy and the Breit correction with the internuclear distance is plotted. The role of relativistic corrections in the proper prediction of the Xe-F distance and the dissociation energy of the molecule is discussed. The problem of the reduction of the number of scalar two-electron integrals is studied. Our results illustrate the possibilities, difficulties, and limitations of the finite basis Dirac-Fock calculations for polyatomic molecules of different symmetries. © 1997 by John Wiley & Sons, Inc.     

Accelerating VASP electronic structure calculations using graphic processing units

We present a way to improve the performance of the electronic structure Vienna Ab initio Simulation Package (VASP) program. We show that high-performance computers equipped with graphics processing units (GPUs) as accelerators may reduce drastically the computation time when offloading these sections to the graphic chips. The procedure consists of (i) profiling the performance of the code to isolate the time-consuming parts, (ii) rewriting these so that the algorithms become better-suited for the chosen graphic accelerator, and (iii) optimizing memory traffic between the host computer and the GPU accelerator. We chose to accelerate VASP with NVIDIA GPU using CUDA. We compare the GPU and original versions of VASP by evaluating the Davidson and RMM-DIIS algorithms on chemical systems of up to 1100 atoms. In these tests, the total time is reduced by a factor between 3 and 8 when running on n (CPU core + GPU) compared to n CPU cores only, without any accuracy loss. © 2012 Wiley Periodicals, Inc.     

ZINDO calculations of the ground state and electronic transitions in the tetracyanonickelate Ion,Ni(CN)(4)(2-)

ZINDO semiempirical calculations on the Ni(CN)(4)(2-) ion were performed, and ground-state energies for all 41 valence-orbital-based MOs and orbital transition components of the two lowest energy fully allowed electronic transitions are reported. Gaussian 94 was used to calculate ground-state energies as a comparison. The ground-state energies using ZINDO compare much more favorably with those found through ab initio techniques than with those from a reported INDO calculation. The found electronic transitions agree substantially with earlier assignments with the exception that several orbital transitions are required to adequately model the lowest energy allowed x,y-polarized experimental transition. Calculation parameters were optimized to give excellent agreement with experiment and may serve well for more complex arrangements of this ion.     

Are Conical Intersections Responsible for the Ultrafast Processes of Adenine,Protonated Adenine,and the Corresponding Nucleosides?

Excited-state potential energy surfaces of adenine, protonated adenine, and their N9-methylated analogs are explored by means of a complete active space (CAS) and time-dependent density functional theory (TD-DFT) study to understand the dynamics associated with internal conversion. After photoexcitation of the ground-state molecules to the S(1) state, the nuclear motions that are responsible for taking the wavepacket out of the Franck-Condon region are either an H--N9/C--N9 stretch or a ring-puckering motion that leads to pyramidalization. These motions lead to accessible conical intersections with the ground-state surface. The results are used to successfully interpret previous measurements on the photodissociation of adenosine 5'-monophosphate nucleotide anions and cations, where the latter react in a highly nonstatistical manner.