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691 results for “Molecular dynamics”

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zenodo44/100

Intrinsic and apparent slip at gas-enriched liquid-liquid interfaces: a molecular dynamics study

- "sl1.dat" : text file with data slip length vs number of gas atoms for k_gas = 1.0 - "sl5.dat" : text file with data slip length vs number of gas atoms for k_gas = 0.5 - "sl25.dat" : text file with data slip length vs number of gas atoms for k_gas = 0.25 - "sl125.dat" : text file with data slip length vs number of gas atoms for k_gas = 0.125 - "plotsl.plt": gnuplot script to plot slip lengths data and obtain figure 5a of the article - "dg.dat": data for solubilities in kbT units from figure 3 of the article - "3600gask0125.xyz": trajectory file in xyz format for the system with k_gas= 0.125 and 3600 gas atoms - "3600.data": starting configuration for k_gas = 0.125 and 3600 gas atoms in restart.data format for lammps - "in.shear": lammps input script to run the shear simulation for the system with k_gas = 0.125 and 3600 gas atoms starting from configuration store in "3600.data" file

opencc-by-4.0Mar 2022View details →

zenodo44/100

Molecular Dynamics simulations of spreading droplets

This dataset contains the results of non-equilibrium Molecular Dynamic simulations of 2-dimensional SPC/E water nanodroplets spontaneously spreading over silica-like walls, performed using Gromacs. The main purpose of these simulations is to study the motion of three-phases contact lines over high-friction surfaces and to test contact line friction models. Further details can be found in 'documentation.pdf'.

opencc-by-4.0Feb 2022View details →

zenodo44/100

data set to bioRxiv preprint 'Persistent cross-species SARS-CoV-2 variant infectivity predicted via comparative molecular dynamics simulation

This is supporting data and software code for the following preprint in bioRxiv Persistent cross-species SARS-CoV-2 variant infectivity predicted via comparative molecular dynamics simulation https://www.biorxiv.org/content/10.1101/2022.04.18.488629v1

opencc-by-4.0Apr 2022View details →

zenodo44/100

Molecular Dynamics simulations of shear droplets

This dataset contains the results of non-equilibrium Molecular Dynamic simulations of 2-dimensional SPC/E water nanodroplets confined between silica-like walls and under shear flow conditions, performed using Gromacs. The main purposes of these simulations are: a) to study the motion of three-phases contact lines over high-friction surfaces, b) to study the critical transition leading to droplet breakage and c) to test the modelling and prediction capabilities of continuous fluid dynamics simulation methods. The investigation of the points above is illustrated in an article, which has been digitally published on the Journal of Fluid Mechanics (doi:10.1017/jfm.2022.219, see references); please refer to the paper for a detailed description of the molecular simulations and of the tested CFD methods. The publication of this dataset not only grants the reproducibility of the results discussed in the article, but also serves as collection of benchmarks for the fellow researchers willing to test improved and/or alternative models to describe the motion of contact lines.

opencc-by-4.0Feb 2022View details →

zenodo44/100

All-atom molecular dynamics simulations of Synechocystis halorhodopsin (SyHR)

The trajectories of all-atom MD simulations of: 1) Cl--bound SyHR in the ground (GR) state (SyHR_monomer_GR_POPC_CHARMM36_200ns) 2) Cl--bound SyHR in the K state (SyHR_monomer_K_POPC_CHARMM36_200ns)  in the monomeric form in a POPC bilayer. 3) SO42--bound SyHR in the GR state (SyHR_trimer_GR_POPC_CHARMM36_500ns) in the trimeric form in a POPC bilayer. Simulations have been performed using the CHARMM36 force field, running with the GROMACS 2022 package.

opencc-by-4.0May 2022View details →

zenodo44/100

Intermolecular interactions in G protein-coupled receptor allosteric sites at the membrane interface from molecular dynamics simulations and quantum chemical calculations

Allosteric modulators are called to be promising candidates in G protein-coupled receptor (GPCR) drug development by displaying target selectivity and fewer side effects. Among the allosteric sites known to date, extrahelical cavities represent an uncharacteristic binding location that raises many questions about the ligand interactions and stability; the binding site structure, and how all of these are affected by lipid molecules. In this work, we analyze the dynamics and interactions in the PAR2, C5aR1, and GCGR receptors unbound and bound to allosteric modulators at the receptor-lipid interface using molecular dynamics simulations in three lipid compositions. In addition, we performed quantum chemical calculations to further explore electrostatic interactions and the strength of atom pairwise contacts in the stabilization of the ligand-receptor complexes. We show that besides classical hydrogen bonds weak polar interactions such as O-HC, O-Br, and S-HC contacts and aromatic interactions contribute to the binding of allosteric modulators at the extrahelical sites in the middle of the membrane. The allosteric cavities are open and detectable in various membrane compositions but not always predicted as druggable.  The availability of polar atoms for interactions in such cavities can be assessed by water molecules from the simulations. Although ligand-lipid interactions are weak, the lipid tails play a role in sizing and shaping the large part of the allosteric cavity.  You will find the following files: <ul> <li>Input files of the equilibration and production protocols of MD simulations (MD_simulations_inputs.zip)</li> <li>Input files and coordinate files of F-SAPT and NCIPLOT calculations (quantum_chemical_coordiates_inputs.zip)</li> </ul>

opencc-by-4.0Jun 2022View details →

zenodo44/100

Ab-initio molecular dynamics trajectories of fully hydrated TiO2 surfaces

This data set contains trajectories of ab-initio molecular dynamics simulations of TiO2 surfaces in water described in the paper: L.Agosta, E.G.Brandt and A.P.Lyubartsev "Diffusion and reaction pathways of water near fully hydrated TiO2 surfaces from ab initio molecular dynamics", J.Chem.Phys., 147, 024704 (2107) doi: http://dx.doi.org/10.1063/1.4991381 Trajectories of 6 fully hydrated TiO2 surfaces are stored under respective names. Each trajectory file contains 50 ps of simulation with frames saved every 0.0005 ps. Format: PDB, gzipped.

opencc-by-4.0Sep 2017View details →

zenodo44/100

Molecular dynamics simulation trajectory of an anionic lipid bilayer: 100 mol% DOPS with Na+ counterions using ff99 Ions

System: Symmetric bilayer of anionic DOPS (1,2-Dioleoyl-sn-glycero-3-phosphoserine 100 mol-%) lipids with sodium (Na+) counter ions. Number of DOPS: 128. Number of Na+-ions: 128. Number of waters: 4480. Lipid model: Amber Lipid 17 [IR Gould, AA Skjevik, CJ Dickson, BD Madej, RC Walker: "Lipid17: A Comprehensive AMBER Force Field for the Simulation of Zwitterionic and Anionic Lipids" in prep. (2018)]. Ion models:  Amber ff99 [J Åqvist J. Phys. Chem. 94 8021 (1990)]. Water model: TIP3P [WL Jorgensen, J Chandrasekhar, JD Madura, RW Impey, ML Klein J. Chem. Phys. 79 926 (1983)]. Simulation engine: Amber16 [DA Case et al. AMBER 2017 UCSF (2017)]. Number of independent repeats per setup: 2. Trajectory lengths per repeat: 400 ns + 100 ns. Previously equilibrated for: 100 ns. Sampling rate: every 10 ps. Time integration step: 2 fs. Thermodynamic ensemble: NpT.  Temperature coupling: 'Langevin' at T = 303 K. Pressure coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984); J. Chem. Phys. 103 10252 (1995)] with xy and z coupled separately at p = 1.0 bar with no surface tension. Electrostatics: PME [J. Chem. Phys. 98 10089 (1993); J. Chem. Theory Comput. 9 3878 (2013)]. Van der Waals: Turned off between 1.0 nm and 1.5 nm. Constraints: Lengths of covalent bonds involving Hydrogens in lipids using SHAKE [J. Comput. Phys. 23 327 (1977)], in water using SETTLE [J. Comput. Chem. 13 952 (1992)]. Used in publications: OHS Ollila et al. "NMRlipids IV: Headgroup & glycerol backbone structures, and cation binding in bilayers with PS lipids" in prep (2018).

opencc-by-4.0Jan 2018View details →

zenodo44/100

Molecular dynamics simulation trajectory of an anionic lipid bilayer: 100 mol% POPS with Na+ counterions using Joung-Cheatham Ions

System: Symmetric bilayer of anionic POPS (palmitoyl-oleoyl-phosphatidylserine 100 mol-%) lipids with sodium (Na+) counter ions. Number of POPS: 128. Number of Na+-ions: 128. Number of waters: 4480. Lipid model: Amber Lipid 17 [IR Gould, AA Skjevik, CJ Dickson, BD Madej, RC Walker: "Lipid17: A Comprehensive AMBER Force Field for the Simulation of Zwitterionic and Anionic Lipids" in prep. (2018)]. Ion model: Joung–Cheatham [IS Joung, TE Cheatham III J. Phys. Chem. B 112 9020 (2008)]. Water model: TIP3P [WL Jorgensen, J Chandrasekhar, JD Madura, RW Impey, ML Klein J. Chem. Phys. 79 926 (1983)]. Simulation engine: Amber16 [DA Case et al. AMBER 2017 UCSF (2017)]. Number of independent repeats per setup: 2. Trajectory lengths per repeat: 400 ns + 100 ns. Previously equilibrated for: 100 ns. Sampling rate: every 10 ps. Time integration step: 2 fs. Thermodynamic ensemble: NpT.  Temperature coupling: 'Langevin' at T = 298 K. Pressure coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984); J. Chem. Phys. 103 10252 (1995)] with xy and z coupled separately at p = 1.0 bar with no surface tension. Electrostatics: PME [J. Chem. Phys. 98 10089 (1993); J. Chem. Theory Comput. 9 3878 (2013)]. Van der Waals: Turned off between 1.0 nm and 1.5 nm. Constraints: Lengths of covalent bonds involving Hydrogens in lipids using SHAKE [J. Comput. Phys. 23 327 (1977)], in water using SETTLE [J. Comput. Chem. 13 952 (1992)]. Used in publications: OHS Ollila et al. "NMRlipids IV: Headgroup & glycerol backbone structures, and cation binding in bilayers with PS lipids" in prep (2018).

opencc-by-4.0Jan 2018View details →

zenodo44/100

Molecular dynamics simulation of SpoIVFB:Pro-SigmaK complex (replicate 1)

Replicate simulation 1/4 Found here are all files needed to reproduce or visualize the results of molecular dynamics simulation of the SpoIVFB intramembrane protease bound to the transcription factor Pro-sigmaK. The protein complex was embedded in a POPE_POPG_DAG_CL bilayer using CHARMM-GUI and simulated using OpenMM. The README file is a C-shell script that will run equilibration and 250ns of unrestrained simulation.  Individual output (.out) and trajectory (.dcd) files are provided for each checkpoint of the simulation. A combined trajectory containing 250 ns of unrestrained simulation is also provided (combined_250ns_traj.dcd). Together with the step5_input.psf file, this combined dcd file can be used with common software such as VMD to visualize the molecular dynamics trajectory.

opencc-by-4.0Jun 2024View details →

zenodo44/100

Molecular dynamics simulation trajectory of an anionic lipid bilayer: 100 mol% POPS with Na+ counterions using ff99 ions

System: Symmetric bilayer of anionic POPS (palmitoyl-oleoyl-phosphatidylserine 100 mol-%) lipids with sodium (Na+) counter ions. Number of POPS: 128. Number of Na+-ions: 128. Number of waters: 4480. Lipid model: Amber Lipid 17 [IR Gould, AA Skjevik, CJ Dickson, BD Madej, RC Walker: "Lipid17: A Comprehensive AMBER Force Field for the Simulation of Zwitterionic and Anionic Lipids" in prep. (2018)]. Ion model: Amber ff99 [J Åqvist J. Phys. Chem. 94 8021 (1990)]. Water model: TIP3P [WL Jorgensen, J Chandrasekhar, JD Madura, RW Impey, ML Klein J. Chem. Phys. 79 926 (1983)]. Simulation engine: Amber16 [DA Case et al. AMBER 2017 UCSF (2017)]. Number of independent repeats per setup: 2. Trajectory lengths per repeat: 400 ns + 100 ns. Previously equilibrated for: 100 ns. Sampling rate: every 10 ps. Time integration step: 2 fs. Thermodynamic ensemble: NpT.  Temperature coupling: 'Langevin' at T = 298 K. Pressure coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984); J. Chem. Phys. 103 10252 (1995)] with xy and z coupled separately at p = 1.0 bar with no surface tension. Electrostatics: PME [J. Chem. Phys. 98 10089 (1993); J. Chem. Theory Comput. 9 3878 (2013)]. Van der Waals: Turned off between 1.0 nm and 1.5 nm. Constraints: Lengths of covalent bonds involving Hydrogens in lipids using SHAKE [J. Comput. Phys. 23 327 (1977)], in water using SETTLE [J. Comput. Chem. 13 952 (1992)]. Used in publications: OHS Ollila et al. "NMRlipids IV: Headgroup & glycerol backbone structures, and cation binding in bilayers with PS lipids" in prep (2018).

opencc-by-4.0Jan 2018View details →

zenodo44/100

Molecular dynamics simulation trajectory of an anionic lipid bilayer: 100 mol% DOPS with Na+ counterions using Joung-Cheetham Ions

System: Symmetric bilayer of anionic DOPS (1,2-Dioleoyl-sn-glycero-3-phosphoserine 100 mol-%) lipids with sodium (Na+) counter ions. Number of DOPS: 128. Number of Na+-ions: 128. Number of waters: 4480. Lipid model: Amber Lipid 17 [IR Gould, AA Skjevik, CJ Dickson, BD Madej, RC Walker: "Lipid17: A Comprehensive AMBER Force Field for the Simulation of Zwitterionic and Anionic Lipids" in prep. (2018)]. Ion models: Joung–Cheatham [IS Joung, TE Cheatham III J. Phys. Chem. B 112 9020 (2008)]. Water model: TIP3P [WL Jorgensen, J Chandrasekhar, JD Madura, RW Impey, ML Klein J. Chem. Phys. 79 926 (1983)]. Simulation engine: Amber16 [DA Case et al. AMBER 2017 UCSF (2017)]. Number of independent repeats per setup: 2. Trajectory lengths per repeat: 400 ns + 100 ns. Previously equilibrated for: 100 ns. Sampling rate: every 10 ps. Time integration step: 2 fs. Thermodynamic ensemble: NpT.  Temperature coupling: 'Langevin' at T = 303 K. Pressure coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984); J. Chem. Phys. 103 10252 (1995)] with xy and z coupled separately at p = 1.0 bar with no surface tension. Electrostatics: PME [J. Chem. Phys. 98 10089 (1993); J. Chem. Theory Comput. 9 3878 (2013)]. Van der Waals: Turned off between 1.0 nm and 1.5 nm. Constraints: Lengths of covalent bonds involving Hydrogens in lipids using SHAKE [J. Comput. Phys. 23 327 (1977)], in water using SETTLE [J. Comput. Chem. 13 952 (1992)]. Used in publications: OHS Ollila et al. "NMRlipids IV: Headgroup & glycerol backbone structures, and cation binding in bilayers with PS lipids" in prep (2018).

opencc-by-4.0Jan 2018View details →

zenodo44/100

A molecular dynamics study of adenylyl cyclase: the impact of ATP and G-protein binding

Adenylyl cyclases (ACs) catalyze the biosynthesis of cyclic adenosine monophosphate (cAMP) from adenosine triphosphate (ATP) and play an important role in many signal transduction pathways. The enzymatic activity of ACs is carefully controlled by a variety of molecules, including G-protein subunits that can both stimulate and inhibit cAMP production. Using homology models developed from existing structural data, we have carried out all-atom, microsecond-scale molecular dynamics simulations on the AC5 isoform of adenylyl cyclase and on its complexes with ATP and with the stimulatory G-protein subunit Gsα. The results show that both ATP and Gsα binding have significant effects on the structure and flexibility of adenylyl cyclase. New data on ATP bound to AC5 in the absence of Gsα notably help to explain how Gsα binding enhances enzyme activity and could aid product release. Simulations also suggest a possible coupling between ATP binding and interactions with the inhibitory G-protein subunit Gαi. All-atom molecular dynamics simulations were performed with the GROMACS 5 package. The simulations were carried out in an NTP ensemble at a temperature of 310 K and a pressure of 1 bar using a Bussi velocity-rescaling thermostat  (tT = 1 ps) and a Parrinello-Rahman barostat (tP = 1 ps).  We provide the atomistic trajectories of the following 6 systems after 400 ns of equilibration: <ul> <li>AC5</li> <li>AC5+ATP</li> <li>AC5+Gsα</li> <li>AC5+ATP+Gsα</li> <li>AC5+FOK</li> <li>AC5+ATP+FOK</li> </ul> In each trajectory, the frames are saved each 20 ps.

opencc-by-4.0Apr 2018View details →

zenodo44/100

Assessment of mutation probabilities of KRAS G12 missense mutants and their long-time scale dynamics by atomistic molecular simulations and Markov state modeling: Datasets.

Datasets related to the publication [1]. Including: <ul> <li>KRAS G12X mutations derived from COSMIC v.79 [http://cancer.sanger.ac.uk/cosmic/] (KRAS_G12X_mut_COSMICv79..xlsx)</li> <li>RMSFs (300-2000ns) of GDP-systems (300_2000rmsf_GDP_systems_RAW_AVG_SE.xlsx)</li> <li>RMSFs (300-2000ns) of GTP-systems (300_2000RMSF_GTP_systems_RAW_AVG_SE.xlsx)</li> <li>PyInteraph analysis data for salt-bridges and hydrophobic clusters (.dat files for each system in the PyInteraph_data.zip-file)</li> <li>Backbone trajectories for each system (residues 4-164; frames for every 1ns). Last number (e.g. _1) refers to the replica of the simulated system.</li> <li>backbone_4-164.gro/.pdb/.tpr -files (resid 4-164)  </li> </ul> [1] Pantsar T et al. Assessment of mutation probabilities of KRAS G12 missense mutants and their long-time scale dynamics by atomistic molecular simulations and Markov state modeling. PLoS Comput Biol Submitted (2018)

opencc-by-4.0Aug 2018View details →

zenodo44/100

Supporting data for "Quantifying the Strength of a Salt Bridge by Neutron Scattering and Molecular Dynamics"

Supporting data for the following published paper: Mason, Jungwirth, Duboué-Dijon, 2019, JPhysChemLett, 10, 3254-3259 Contains both data from neutron scattering measurements and input simulation files necessary for reproduction of the work.

opencc-by-4.0Jun 2019View details →

zenodo44/100

Molecular dynamics simulations of the interaction of the quadruple mutant human CYP2J2 (R111A + R117A + R382A + R446A) with arachidonic acid (POSES 1-3)

Description of files in this dataset: MD_quadmut_CYP2J2_AA_StateX_repeatY.zip : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of the quadruple R111A + R117A+R382A+R446A) mutant CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose).   Each directory contains the following sub-directories: 001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands 002.min : Minimisation stage 003.heat : Heating stage 004.equil: Equilibration stage

opencc-by-4.0Oct 2019View details →

zenodo44/100

Molecular dynamics simulations of the interaction of mutant human CYP2J2 (R117A) with arachidonic acid (POSES 5-6)

Description of files in this dataset: MD_mutR117A_CYP2J2_AA_StateX_repeatY.zip : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of the R117A mutant CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose).   Each directory contains the following sub-directories: 001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands 002.min : Minimisation stage 003.heat : Heating stage 004.equil: Equilibration stage 005.md : Production stage 006.analysis : Basic energy graphs 007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)

opencc-by-4.0Oct 2019View details →

zenodo44/100

Molecular dynamics simulations of the interaction of wild type human CYP2J2 with DHA (POSES 1-4)

Description of files in this dataset: MD_wt_CYP2J2_DHA_StateX_repeatY.zip : Series of zipped directories for molecular dynamics simulations of docosahexaenoic acid (DHA) in the active site of wild type CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 4 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose).   Each directory contains the following sub-directories: 001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands 002.min : Minimisation stage 003.heat : Heating stage 004.equil: Equilibration stage 005.md : Production stage 006.analysis : Basic energy graphs 007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)

opencc-by-4.0Oct 2019View details →

zenodo44/100

Molecular dynamics simulations of the interaction of wild type human CYP2J2 with arachidonic acid (POSES 3 and 4)

Description of files in this dataset: MD_wt_CYP2J2_AA_StateX_repeatY.zip : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of wild type CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 4 times, hence there are 4 repeats per pose).   Each directory contains the following sub-directories: 001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands 002.min : Minimisation stage 003.heat : Heating stage 004.equil: Equilibration stage 005.md : Production stage 006.analysis : Basic energy graphs 007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)

opencc-by-4.0Sep 2019View details →

zenodo44/100

Homology modelling, molecular docking and molecular dynamics simulations of wild type and mutant human CYP2J2 with three polyunsaturated fatty acids

This is the "parent" repository for the Data Note : "Molecular dynamics simulations of the interaction of wild type and mutant human CYP2J2 with polyunsaturated fatty acids" by Abelak, Bishop-Bailey and Nobeli. It contains a document (Abelak_etal_Methods.pdf) describing the methods used to produce the data here and the data in all repositories supplementing it. It also contains a shell script (create_sim4_repeats.sh) that is typical of those used to set up the molecular dynamics simulations in the repositories supplementing this one. Finally, it contains the results of the homology modelling and docking simulations that formed the starting points for the molecular dynamics simulations in this study. Description of files in this dataset: C2J2_min3_mod_noH.pdb : Homology model of the wild type CYP2J2 built from an alignment of templates with PDB ids: 1SUO, 2P85, 3EBS and 1Z10. docking_wild_type_C2J2.zip : Nine docked poses of arachidonic acid docked to the homology model of the wild type CYP2J2. Details of how this data was produced is available in the Abelak_etal_Methods.docx document.

opencc-by-4.0Sep 2019View details →

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Last verified 2026-04-29Open record