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Most commonly, by writing the constituent B, C, N, O, P and S atoms in lower-case forms b, c, n, o, p and s, respectively. In the latter case, bonds between two aromatic atoms are assumed (if not explicitly shown) to be aromatic bonds. Thus, benzene, pyridine and furan can be represented respectively by the SMILES c1ccccc1, n1ccccc1 and o1cccc1.
OPLS simulations in aqueous solution typically use the TIP4P or TIP3P water model. A distinctive feature of the OPLS parameters is that they were optimized to fit experimental properties of liquids, such as density and heat of vaporization, in addition to fitting gas-phase torsional profiles.
High performance GPU-accelerated ab initio molecular dynamics and TD/DFT software package for very large molecular or even nanoscale systems. Runs on NVIDIA GPUs and 64-bit Linux, has heavily optimized CUDA code. Proprietary, trial licenses available PetaChem LLC: TINKER: I Yes Yes Yes Yes I I Yes Yes Software tools for molecular design-Tinker ...
List of software for Monte Carlo molecular modeling; Comparison of software for molecular mechanics modeling; Molecular design software; Molecule editor; Molecular modeling on GPUs; List of software for nanostructures modeling; Semi-empirical quantum chemistry method; Computational chemical methods in solid-state physics, with periodic boundary ...
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Scilab - free open-source software for numerical computation and simulation similar to MATLAB/Simulink. SDC Verifier - structural design and finite element analysis software with a calculation core for checking structures according to different standards, either predefined or self programmed, and final report generation with all checks.
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