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Publication Year: 2023 Keyword Term: Molecular Dynamics Simulation Keyword Term: GROMACS

1 to 5 of 5 Results

Molecular simulation scripts for slit nanopores with tunable hydrophilicity Oct 11, 2023 - NMR insights into nanoconfined water using the surface exchange model Gravelle, Simon, 2023, "Molecular simulation scripts for slit nanopores with tunable hydrophilicity", https://doi.org/10.18419/darus-3732, DaRUS, V1 GROMACS molecular simulation input files for slit nanopores filled with liquid water. Initial configuration can be generated using the Python script build_system.py. Use the bash script run_gmx.sh to run GROMACS. See the README.md file.
Scripts for "Assessing the validity of NMR relaxation rates obtained from coarse-grained simulations" Mar 13, 2023 - Holm group Gravelle, Simon; Beyer, David; Brito, Mariano E.; Schlaich, Alexander; Holm, Christian, 2023, "Scripts for "Assessing the validity of NMR relaxation rates obtained from coarse-grained simulations"", https://doi.org/10.18419/darus-3313, DaRUS, V1 Simulations and data analysis scripts for the publication "Assessing the validity of NMR relaxation rates obtained from coarse-grained simulations". The dataset contains two types of simulation scripts: all-atom simulation (GROMACS) and coarse-grained simulations (ESPRESSO). In b...
Molecular simulation scripts for slit nanopores Mar 9, 2023 - NMR investigation of water confined by salt interface Gravelle, Simon; Holm, Christian; Schlaich, Alexander, 2023, "Molecular simulation scripts for slit nanopores", https://doi.org/10.18419/darus-3180, DaRUS, V1 GROMACS molecular simulation input files for slit nanopores made of NaCl and Na2SO4 solid walls, and filled with respectively NaCl and Na2SO4 solutions. Initial configuration with a given salt concentration can be generated using the Python script ConfigurationGenerator.py, and s...
Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death' Mar 9, 2023 - PN 3-11 Degen, Morris; Santos, José Carlos; Pluhackova, Kristyna; Cebrero, Gonzalo; Ramos, Saray; Jankevicius, Gytis; Hartenian, Ella; Guillerm, Undina; Mari, Stefania A.; Kohl, Bastian; Müller, Daniel J.; Schanda, Paul; Maier, Timm; Perez, Camilo; Sieben, Christian; Broz, Petr; Hiller, Sebastian, 2023, "Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'", https://doi.org/10.18419/darus-3373, DaRUS, V1 Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture (PMR) as the defining terminal event. PMR was long thought to be driven by osmotic pressure, until it was recently shown to be in many cases an active process...
Molecular simulation scripts for bulk solutions Mar 8, 2023 - NMR investigation of water confined by salt interface Gravelle, Simon; Holm, Christian; Schlaich, Alexander, 2023, "Molecular simulation scripts for bulk solutions", https://doi.org/10.18419/darus-3179, DaRUS, V1 GROMACS molecular simulation input files for bulk solutions of NaCl and Na2SO4. Initial configuration with different salt concentration can be generated using the Python script ConfigurationGenerator.py, and successive GROMACS runs can be performed by running the runall.sh Bash s...

Molecular simulation scripts for slit nanopores with tunable hydrophilicity

Oct 11, 2023 - NMR insights into nanoconfined water using the surface exchange model

Gravelle, Simon, 2023, "Molecular simulation scripts for slit nanopores with tunable hydrophilicity", https://doi.org/10.18419/darus-3732, DaRUS, V1

GROMACS molecular simulation input files for slit nanopores filled with liquid water. Initial configuration can be generated using the Python script build_system.py. Use the bash script run_gmx.sh to run GROMACS. See the README.md file.

Scripts for "Assessing the validity of NMR relaxation rates obtained from coarse-grained simulations"

Mar 13, 2023 - Holm group

Gravelle, Simon; Beyer, David; Brito, Mariano E.; Schlaich, Alexander; Holm, Christian, 2023, "Scripts for "Assessing the validity of NMR relaxation rates obtained from coarse-grained simulations"", https://doi.org/10.18419/darus-3313, DaRUS, V1

Simulations and data analysis scripts for the publication "Assessing the validity of NMR relaxation rates obtained from coarse-grained simulations". The dataset contains two types of simulation scripts: all-atom simulation (GROMACS) and coarse-grained simulations (ESPRESSO). In b...

Molecular simulation scripts for slit nanopores

Mar 9, 2023 - NMR investigation of water confined by salt interface

Gravelle, Simon; Holm, Christian; Schlaich, Alexander, 2023, "Molecular simulation scripts for slit nanopores", https://doi.org/10.18419/darus-3180, DaRUS, V1

GROMACS molecular simulation input files for slit nanopores made of NaCl and Na2SO4 solid walls, and filled with respectively NaCl and Na2SO4 solutions. Initial configuration with a given salt concentration can be generated using the Python script ConfigurationGenerator.py, and s...

Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'

Mar 9, 2023 - PN 3-11

Degen, Morris; Santos, José Carlos; Pluhackova, Kristyna; Cebrero, Gonzalo; Ramos, Saray; Jankevicius, Gytis; Hartenian, Ella; Guillerm, Undina; Mari, Stefania A.; Kohl, Bastian; Müller, Daniel J.; Schanda, Paul; Maier, Timm; Perez, Camilo; Sieben, Christian; Broz, Petr; Hiller, Sebastian, 2023, "Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'", https://doi.org/10.18419/darus-3373, DaRUS, V1

Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture (PMR) as the defining terminal event. PMR was long thought to be driven by osmotic pressure, until it was recently shown to be in many cases an active process...

Molecular simulation scripts for bulk solutions

Mar 8, 2023 - NMR investigation of water confined by salt interface

Gravelle, Simon; Holm, Christian; Schlaich, Alexander, 2023, "Molecular simulation scripts for bulk solutions", https://doi.org/10.18419/darus-3179, DaRUS, V1

GROMACS molecular simulation input files for bulk solutions of NaCl and Na2SO4. Initial configuration with different salt concentration can be generated using the Python script ConfigurationGenerator.py, and successive GROMACS runs can be performed by running the runall.sh Bash s...

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