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Jayaraman Chandrasekhar

Bio: Jayaraman Chandrasekhar is a academic researcher at Indian Institute of Science who has co-authored 235 publication(s) receiving 41956 citation(s). The author has an hindex of 44. Previous affiliations of Jayaraman Chandrasekhar include Yale University & Indian Institute of Technology Madras. The author has done significant research in the topic(s): Ab initio & Molecular orbital.

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Topics: Ab initio, Molecular orbital, Excited state ...read more
Papers
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Journal ArticleDOI: 10.1063/1.445869
Abstract: Classical Monte Carlo simulations have been carried out for liquid water in the NPT ensemble at 25 °C and 1 atm using six of the simpler intermolecular potential functions for the water dimer: Bernal–Fowler (BF), SPC, ST2, TIPS2, TIP3P, and TIP4P. Comparisons are made with experimental thermodynamic and structural data including the recent neutron diffraction results of Thiessen and Narten. The computed densities and potential energies are in reasonable accord with experiment except for the original BF model, which yields an 18% overestimate of the density and poor structural results. The TIPS2 and TIP4P potentials yield oxygen–oxygen partial structure functions in good agreement with the neutron diffraction results. The accord with the experimental OH and HH partial structure functions is poorer; however, the computed results for these functions are similar for all the potential functions. Consequently, the discrepancy may be due to the correction terms needed in processing the neutron data or to an effect uniformly neglected in the computations. Comparisons are also made for self‐diffusion coefficients obtained from molecular dynamics simulations. Overall, the SPC, ST2, TIPS2, and TIP4P models give reasonable structural and thermodynamic descriptions of liquid water and they should be useful in simulations of aqueous solutions. The simplicity of the SPC, TIPS2, and TIP4P functions is also attractive from a computational standpoint.

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Topics: Water model (53%), Solvent models (52%), Water dimer (51%) ...read more

29,424 Citations


Journal ArticleDOI: 10.1002/JCC.540040303
Abstract: The relatively small diffuse function-augmented basis set, 3-21+G, is shown to describe anion geometries and proton affinities adequately. The diffuse sp orbital exponents are recommended for general use to augment larger basis sets.

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Topics: STO-nG basis sets (59%), Basis set (51%), Basis (linear algebra) (50%)

5,374 Citations




Journal ArticleDOI: 10.1021/JA960136Q
Abstract: First hyperpolarizabilities of a large number of push−pull substituted conjugated systems with heteroaromatic spacers have been calculated. The static, nonresonant components were computed at the ab initio level (4-31G basis) using the coupled perturbed Hartree−Fock approach and at the AM1 level employing the finite field method. Sum-over-states procedure has also been used with the AM1/CI method to compute β0 and β at an excitation energy of 1.17 eV. The computed β values at the various levels are reasonably similar and exhibit the same trends. The largest values are obtained with a donor on pyrrole and an acceptor on thiophene or thiazole. The variations do not always inversely follow the order of delocalization energies of the heterocyclic rings. The trends in the dipole moment changes and transition energies between the ground and first excited charge-transfer state primarily determine the variations in the computed β values.

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Topics: Excited state (52%), Ab initio (51%)

268 Citations


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Journal ArticleDOI: 10.1063/1.470117
Ulrich Essmann1, Lalith Perera1, Max L. Berkowitz, Tom Darden2  +2 moreInstitutions (2)
Abstract: The previously developed particle mesh Ewald method is reformulated in terms of efficient B‐spline interpolation of the structure factors This reformulation allows a natural extension of the method to potentials of the form 1/rp with p≥1 Furthermore, efficient calculation of the virial tensor follows Use of B‐splines in place of Lagrange interpolation leads to analytic gradients as well as a significant improvement in the accuracy We demonstrate that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N) For biomolecular systems with many thousands of atoms this method permits the use of Ewald summation at a computational cost comparable to that of a simple truncation method of 10 A or less

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Topics: P3M (68%), Ewald summation (66%), Particle Mesh (56%) ...read more

15,288 Citations


Open accessJournal ArticleDOI: 10.1021/CT700301Q
Abstract: Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions Not only does this combination of a

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  • Figure 5. Performance for lysozyme in water (24119 atoms) with OPLS-aa and PME on a 3 GHz dual core Intel Core2 cluster with 2 (solid lines) and 4 (dashed lines) cores per InFIniband interconnect. The dot-dashed line indicates linear scaling.
    Figure 5. Performance for lysozyme in water (24119 atoms) with OPLS-aa and PME on a 3 GHz dual core Intel Core2 cluster with 2 (solid lines) and 4 (dashed lines) cores per InFIniband interconnect. The dot-dashed line indicates linear scaling.
  • Table 3. Number of Steps per Second for a Coarse-Grained Polystyrene Modela
    Table 3. Number of Steps per Second for a Coarse-Grained Polystyrene Modela
  • Table 1. Number of MD Steps per Second with and without Spatial Sorting of Charge Groupsa
    Table 1. Number of MD Steps per Second with and without Spatial Sorting of Charge Groupsa
  • Table 5. Simulation Speed in ns/day with GROMACS 4 Domain Decomposition and GROMACS 3.3 Particle Decomposition for the Membrane/Protein System (121449 Atoms)a
    Table 5. Simulation Speed in ns/day with GROMACS 4 Domain Decomposition and GROMACS 3.3 Particle Decomposition for the Membrane/Protein System (121449 Atoms)a
  • Table 4. Parameters for the DHFR Benchmark and the Energy Drift per Degree of Freedom
    Table 4. Parameters for the DHFR Benchmark and the Energy Drift per Degree of Freedom
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Topics: Particle Mesh (50%)

12,609 Citations


Journal ArticleDOI: 10.1021/JP973084F
Abstract: New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent−solvent, solvent−solute, and solute−solute interactions. Optimization of the internal parameters used experimental gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes between water and model compounds that represented the backbone and the various side chains. In addition, dipole moments, experimental heats and free energies of vaporization, solvation and sublimation, molecular volume...

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Topics: Ab initio (59%), Force field (chemistry) (53%), Solvation (53%) ...read more

12,333 Citations


Journal ArticleDOI: 10.1002/JCC.20291
David van der Spoel1, Erik Lindahl2, Berk Hess3, Gerrit Groenhof4  +2 moreInstitutions (4)
Abstract: This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org.

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Topics: Software suite (50%)

10,642 Citations


Journal ArticleDOI: 10.1021/JA9621760
Abstract: The parametrization and testing of the OPLS all-atom force field for organic molecules and peptides are described. Parameters for both torsional and nonbonded energetics have been derived, while the bond stretching and angle bending parameters have been adopted mostly from the AMBER all-atom force field. The torsional parameters were determined by fitting to rotational energy profiles obtained from ab initio molecular orbital calculations at the RHF/6-31G*//RHF/6-31G* level for more than 50 organic molecules and ions. The quality of the fits was high with average errors for conformational energies of less than 0.2 kcal/mol. The force-field results for molecular structures are also demonstrated to closely match the ab initio predictions. The nonbonded parameters were developed in conjunction with Monte Carlo statistical mechanics simulations by computing thermodynamic and structural properties for 34 pure organic liquids including alkanes, alkenes, alcohols, ethers, acetals, thiols, sulfides, disulfides, a...

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Topics: Ab initio (56%), Free energy perturbation (52%), Molecular orbital (50%)

10,389 Citations


Performance
Metrics

Author's H-index: 44

No. of papers from the Author in previous years
YearPapers
20207
20193
20181
20172
20163
20141

Top Attributes

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Author's top 5 most impactful journals

ChemInform

40 papers, 104 citations

Journal of the American Chemical Society

34 papers, 3.5K citations

Journal of Organic Chemistry

12 papers, 299 citations

Chemical Physics Letters

10 papers, 175 citations

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