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BMC research notes, ISSN 1756-0500, 2012, Volume 5, Issue 1, pp. 367 - 367
Journal Article
Journal of computational chemistry, ISSN 0192-8651, 09/2007, Volume 28, Issue 12, pp. 2075 - 2084
We investigate the parallel scaling of the GROMACS molecular dynamics code on Ethernet Beowulf clusters and what prerequisites are necessary for decent scaling... 
MPI_Alltoall | Ethernet flow control | GROMACS parallel molecular dynamics | Car‐Parrinello MD | network congestion | Network congestion | Car-Parrinello MD
Journal Article
Proceedings of the National Academy of Sciences - PNAS, ISSN 1091-6490, 04/2011, Volume 108, Issue 17, pp. 6838 - 6842
Water is a demanding partner. It strongly attracts ions, yet some halide anions— chloride, bromide, and iodide—are expelled to the air/water interface. This... 
Alkalies | Molecules | Anions | Solvation | Halides | Molecular dynamics | Ions | Cations | Entropy | Free energy | Thermodynamics | Ozone layer | GROMACS | Aerosol | Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Water chemistry | Atmospheric chemistry | Atomic properties | Research | Chemical properties | thermodynamics | Physical Sciences | ozone layer | aerosol
Journal Article
Journal of computational chemistry, ISSN 1096-987X, 07/2019, Volume 40, Issue 27, pp. 2418 - 2431
We identify hardware that is optimal to produce molecular dynamics (MD) trajectories on Linux compute clusters with the GROMACS 2018 simulation package.... 
CUDA | energy efficiency | computer simulations | molecular dynamics | performance to price | GPU | parallel computing | GROMACS | high throughput MD | benchmark | Physical Sciences | Chemistry | Chemistry, Multidisciplinary | Science & Technology | Molecular dynamics | Index Medicus
Journal Article
Soft matter, ISSN 1744-683X, 2016, Volume 12, Issue 23, pp. 5164 - 5171
Journal Article
Journal of computational chemistry, ISSN 0192-8651, 08/2011, Volume 32, Issue 11, pp. 2359 - 2368
The drug discovery process has been deeply transformed recently by the use of computational ligand‐based or structure‐based methods, helping the lead compounds... 
force field | small molecule | www.swissparam.ch | topology | CHARMM | parameters | GROMACS | EADock | Physical Sciences | Chemistry | Chemistry, Multidisciplinary | Science & Technology | Thermodynamics | Proteins - metabolism | Organic Chemicals | Small Molecule Libraries | Computer Simulation | Protein Binding | Proteins - chemistry | Drug Discovery | Index Medicus
Journal Article
Carbohydrate polymers, ISSN 0144-8617, 09/2018, Volume 196, pp. 56 - 65
•Elucidation of mechanisms describing the complexation of amylose and linoleic acid.•Amylose acquires a V-type helical conformation in the presence of linoleic... 
Complexation | Gromacs | Amylose | Molecular dynamics simulation | Stearic acid | Linoleic acid | Physical Sciences | Chemistry | Chemistry, Organic | Polymer Science | Chemistry, Applied | Science & Technology | Unsaturated fatty acids | Linoleic acids | Hydrogen | Analysis | Molecular dynamics | Polyphenols | Glucose | Saturated fatty acids | Dextrose | Index Medicus
Journal Article
Journal of physics. Condensed matter, ISSN 0953-8984, 11/2017, Volume 29, Issue 50, pp. 504002 - 504002
Biological membranes are continuously remodeled in the cell by specific membrane-shaping machineries to form, for example, tubes and vesicles. We examine... 
envelope | GROMACS | virus | Dengue | simulation | Physics, Condensed Matter | Physical Sciences | Physics | Science & Technology | Cell Membrane - chemistry | Protein Structure, Secondary | Dengue Virus - chemistry | Viral Envelope Proteins - chemistry | Molecular Dynamics Simulation | Index Medicus
Journal Article
Journal of physics. Condensed matter, ISSN 0953-8984, 07/2016, Volume 28, Issue 39, pp. 394002 - 394002
Natural asphaltenes are defined as polyaromatic compounds whose chemical composition and structure are dependent on their geological origin and production... 
aggregation | asphaltenes | GROMACS | polyaromatic | Physics, Condensed Matter | Physical Sciences | Physics | Science & Technology | Asphaltenes | Molecular structure | Computer simulation | Condensed matter | Molecular dynamics | Dimers | Agglomeration | Aliphatic compounds
Journal Article
Journal of computational chemistry, ISSN 0192-8651, 10/2012, Volume 33, Issue 27, pp. 2204 - 2208
OBGMX is a web service providing topologies for the GROMACS molecular dynamics software package according to the Universal Force Field, as implemented in the... 
molecular topologies | metal‐organic frameworks | periodic systems | universal force field | GROMACS | metal-organic frameworks | Physical Sciences | Chemistry | Chemistry, Multidisciplinary | Science & Technology | Organometallic Compounds - chemistry | Software | Molecular Dynamics Simulation | Index Medicus
Journal Article
Journal of the Brazilian Chemical Society, ISSN 0103-5053, 2008, Volume 19, Issue 7, pp. 1433 - 1435
Molecular mechanics methods are widely-used for simulations of biomolecules. A molecular topology file containing all atom types, which depend on the chemical... 
Molecular mechanics | Molecular topology | Atom-type recognition | GROMACS | OPLS | Physical Sciences | Chemistry | Chemistry, Multidisciplinary | Science & Technology
Journal Article