Search Results for "solvent"
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Showing 13 open source projects for "solvent"
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GROMACS
Public/backup repository of the GROMACS molecular simulation toolkit
GROMACS is a molecular simulation toolkit focused on high-performance molecular dynamics. It is widely used for biomolecular systems such as proteins, lipids, nucleic acids, solvents, and ligand interactions. The software is optimized for speed and supports modern CPU and GPU acceleration for large and demanding simulations. It includes tools for system preparation, running simulations, trajectory processing, analysis, and workflow automation. GROMACS is especially strong in computational... -
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CS-NPSA
Nonpolar Surface Area from Continuum Solvation
The Continuum Solvation Nonpolar Surface Area (CS-NPSA) package is a general purpose program suite for defining and computing nonpolar surface areas based on continuum solvation models. It is based on the classification of individual surface elements representing the solvent accessible surface used for the description of the polarized charge density elements in the CS models. -
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APBS
Biomolecular electrostatics software
This software has moved to http://www.poissonboltzmann.org/. -
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TARQUIN
MRS/NMR analysis software
Analysis software for MRS/NMR data. Allows processing and fitting to be performed in a fully automatic workflow. -
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pyMDMix
Molecular dynamics with aqueous-organic solvent mixtures
This python package aims to help people set up and analyze molecular dynamics simulations in aqueous-organic solvent mixtures. See D. Alvarez-Garcia et al. Journal of Medicinal Chemistry, 2014. -
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GROsolEv4.5
Calculates pairwise energies from Gromacs simulations.
Calculates intermolecular energies for solvent-solvent interactions, for solvent confined to environments a few angstroms in diameter. Algorithm uses a spherical approximation to describe the confined environments geometry. -
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sphrheo
SPH add-on to LAMMPS for the rheology of Non-Newtonian liquids
...At the current stage, it provides libraries for strain-rate dependent viscosity, a dynamic stress model (Rolie-Poly), and the inclusion of colloidal particles in a viscoelastic solvent. -
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SABLE is a public domain package for structural bioinformatics that can be used to predict from amino acid sequence secondary structure and solvent accessibility profiles in proteins (see Adamczak, Porollo and Meller, Proteins 56, 2004).
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piv_clustering
structural clustering of atomic trajectories based on PIV
...At variance with other approaches, it is possible to analyse also processes in solution, e.g., chemical reactions in liquid water, since the distance metric is based on a Permutation Invariant Vector (PIV) that is symmetric under exchange of identical atoms or molecules, including on the same footing both solute and solvent degrees of freedom. The approach is general and the definition of PIV only requires to specify the range of interatomic distances that is relevant for the process under study. Alternatively, also the SPRINT topological coordinates can be employed, that are particularly suited for nanostructures. The output is a partitioning of the trajectory into a few structural clusters (i.e., sets of frames), allowing for simpler analysis and visualization. ... -
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PreDyJE
PreDyJE is a python tool to calculate dehydrons in a protein.
PreDyJE is a python tool to calculate dehydrons in a protein PDB. Dehydrons are solvent-exposed hydrogen bonds. It runs in command-line, but a Pymol script has been developed as well. Dehydrons can be visualized in Pymol with another plugin. Structure of the program is available in the documentation. -
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Protein Stability
VIRTUAL QUANTIFICATION OF PROTEIN STABILITY
...To the best of our knowledge, Protein Stability is a first program of its kind, developed to explore the energy requirement of each amino acid in the protein sequence derived from various applied kinetic and thermodynamic quantities. The algorithm is strongly dependent both on kinetic quantities such as atomic solvation energies and solvent accessible surface area and thermodynamic quantities viz. enthalpy, entropy, heat capacity, etc. The hydrophobicity pattern of protein was considered as the important component of protein stabilization. A program -
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The Solvent is a cross-browser AJAX application toolkit written in JavaScript. The Solvent is provided as modules or as an entire toolkit. The projects focus is to promote robust web applications and enable rapid web development.
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POllution PRevention Of Processes - optimizes chemical processes towards pollution prevention (a. solvent selection, b. waste minimization), when basic process data is given
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