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41 results for “atomistic simulation”
Atomistic Fingerprint of Hyaluronan-CD44 Binding: Unbound Simulations, Set 2
<p>Simulation files (Gromacs 4.6.7 format) for the "Unbound" simulations in Ref. [1]. There are two replicas marked with "_4" and "_5".</p> <p>Files include:</p> <p>-trajectories (.xtc) that are saved every 100ps <br> -initial structures (.gro), <br> -run input files (.tpr)<br> -checkpoint files (.cpt)<br> -simulation parameter files (.mdp)<br> -system topology file (.top)<br> -topology files included in the system topology file (.itp)</p> <p>[1] Vuorio J. et al., Atomistic Fingerprint of Hyaluronan-CD44 Binding, PLOS Comp. Biol., 2017. (Submitted)</p>
Atomistic Fingerprint of Hyaluronan-CD44 Binding: Unbound Simulations, Set 1
<p>Simulation files (Gromacs 4.6.7 format) for the "Unbound" simulations in Ref. [1]. There are three replicas marked with "_1" , "_2", and "_3".</p> <p>Files include:</p> <p>-trajectories (.xtc) that are saved every 100ps <br> -initial structures (.gro), <br> -run input files (.tpr)<br> -checkpoint files (.cpt)<br> -simulation parameter files (.mdp)<br> -system topology file (.top)<br> -topology files included in the system topology file (.itp)</p> <p>[1] Vuorio J. et al., Atomistic Fingerprint of Hyaluronan-CD44 Binding, PLOS Comp. Biol., 2017. (Submitted)</p>
Atomistic Fingerprint of Hyaluronan-CD44 Binding: Clustering Simulations
<p>Simulation files (Gromacs 4.6.7 format) for the "Clustering" simulations in Ref. [1]. There are two replicas marked with "_1" and "_2".</p> <p>Files include:</p> <p>-trajectories (.xtc) that are saved every 100ps <br> -initial structures (.gro), <br> -run input files (.tpr)<br> -checkpoint files (.cpt)<br> -simulation parameter files (.mdp)<br> -system topology file (.top)<br> -topology files included in the system topology file (.itp)</p> <p>[1] Vuorio J. et al., Atomistic Fingerprint of Hyaluronan-CD44 Binding, PLOS Comp. Biol., 2017. (Submitted)</p>
Atomistic Fingerprint of Hyaluronan-CD44 Binding: Strong E-field Simulations
<p>Simulation files (Gromacs 4.6.7 format) for the "E-field strong" simulations in Ref. [1]. There are four different systems ("Crystallographic A-form", "Crystallographic B-form", "Parallel", "Upright") with 20 replica simulations in each (marked with "_1" etc.).</p> <p>Files include:</p> <p>-trajectories (.xtc) that are saved every 100ps <br> -initial structures (.gro), <br> -run input files (.tpr)<br> -checkpoint files (.cpt)<br> -simulation parameter files (.mdp)<br> -system topology file (.top)<br> -topology files included in the system topology file (.itp)</p> <p>[1] Vuorio J. et al., Atomistic Fingerprint of Hyaluronan-CD44 Binding, PLOS Comp. Biol., 2017. (Submitted)</p>
Atomistic Fingerprint of Hyaluronan-CD44 Binding: Seeding Simulations
<p>Simulation files (Gromacs 4.6.7 format) for the "Seeding" simulations in Ref. [1].</p> <p>Files include:</p> <p>-trajectories (.xtc) that are saved every 100ps <br> -initial structures (.gro), <br> -run input files (.tpr)<br> -checkpoint files (.cpt)<br> -simulation parameter files (.mdp)<br> -system topology file (.top)<br> -topology files included in the system topology file (.itp)</p> <p>[1] Vuorio J. et al., Atomistic Fingerprint of Hyaluronan-CD44 Binding, PLOS Comp. Biol., 2017. (Submitted)</p>
Atomistic Fingerprint of Hyaluronan-CD44 Binding: Gathering Simulations
<p>Simulation files (Gromacs 4.6.7 format) for the "Gathering" simulations in Ref. [1].</p> <p>Files include:</p> <p>-trajectories (.xtc) that are saved every 100ps <br> -initial structures (.gro), <br> -run input files (.tpr)<br> -checkpoint files (.cpt)<br> -simulation parameter files (.mdp)<br> -system topology file (.top)<br> -topology files included in the system topology file (.itp)</p> <p>[1] Vuorio J. et al., Atomistic Fingerprint of Hyaluronan-CD44 Binding, PLOS Comp. Biol., 2017. (Submitted)</p>
Dataset for Atomistic simulations on liquid Mg-Sr alloys assisted with deep learning potential
<p>This Dataset is for the paper "Atomistic simulations on liquid Mg-Sr alloys assisted with deep learning potential," including an example script, interatomic potentials, and training data.</p>
Research data supporting: "Exploring RNA destabilization mechanisms in biomolecular condensates through atomistic Simulations"
<p>This repository contains the data to reproduce the results shown in the bioRxiv preprint "Exploring RNA Destabilization Mechanisms in Biomolecular Condensates through Atomistic Simulations" (DOI: 10.1101/2024.09.13.612876).</p>
GPUMD: A package for constructing accurate machine-learned potentials and performing highly efficient atomistic simulations
<p>Supplementary data for the paper "GPUMD: A package for constructing accurate machine-learned potentials and performing highly efficient atomistic simulations" by the GPUMD developers.</p>
Atomistic simulations of the adenosine A2 receptor in membranes with varying levels of SDPE
<p>An adenosine A2 receptor was simulated in membranes consisting of DSPC, cholesterol (20 mol%), and varying levels (0, 4, or 8 mol%) of SDPE with a polyunsaturated chain. Upon increasing SDPE concentration, the concentration of DSPC was correspondingly decreased. The initial structures for these simulations were obtained from the final structures of corresponding coarse-grained simulations, where an SDPE-rich corona formed around the receptor. After fine-graining, the systems were simulated using the CHARMM36 [1] force field for 200 ns using the GROMACS package [2].</p> <p>These simulations were also repeated in the absence of protein. These systems were set up using the CHARMM-GUI web portal [3]. The corresponding files have the 'NOPROT' suffix, and the simulation parameter file is called md_noprot.mdp.</p> <p>For details on the fine-graining and the simulation protocol, please see the related paper at DOI: 10.1371/journal.pcbi.1007033.</p> <p>The files named PUFA_X.* correspond to simulations with X mol% of SDPE with the protein, whereas the files names PUFA_X_NOPROT.* are the corresponding files in the absence of the protein. For each concentration, a run input file (tpr) and the simulation outputs (xtc, edr, log, gro) are provided. Moreover, the simulations can be extended using the provided cpt files.</p> <p>Moreover, the files required to generate the run input file are also provided. For each system, a topology file (top) and an index file (ndx) are provided. The CHARMM36 force field and the molecule definitions (itp) referenced by the topology are also provided. The used simulation parameters are provided in the md.mdp file. For the fine-graining of SDPE, the mapping file is also provided (sdpe.charmm36.map).</p> <p>[1] <strong>DOI: </strong>10.1021/jp101759q</p> <p>[2] <strong>DOI: </strong>10.1016/j.softx.2015.06.001</p> <p>[3] <strong>DOI: </strong>10.1021/acs.jctc.5b00935</p>
Atomistic simulations of DAPC/cholesterol bilayers with one cholesterol restrained to the membrane core
<p>Membranes consisting of 260 DAPC and 28 (10 mol%) cholesterol molecules were simulated at various temperatures of 285, 298, 310, 320, and 333 K. Notably, one cholesterol molecule was restrained to the membrane core. The CHARMM36 force field [1] was used and the membranes were generated using CHARMM-GUI [2].</p> <p>For simulations without a restrained cholesterol, see the other upload at DOI:</p> <p>The simulations were run for 2 microseconds using the GROMACS simulation suite [3]. Simulation parameters are found in the common mdp file (note that the temperature varies between simulations).</p> <p>The upload contains simulation inputs and outputs that allows the replication, extension, or analysis of the simulation data:</p> <ul> <li>Topology files (top) and molecular definitions (itp)</li> <li>Index files (ndx)</li> <li>A common run parameter file (mdp)</li> <li>A run input file (tpr)</li> <li>Trajectory file (xtc) written every 100 ps</li> <li>Energy file (edr)</li> <li>Log file (log)</li> <li>Final structure file (gro)</li> <li>Continue point file (cpt)</li> </ul> <p>The files are named LLLL_AA_CHOLXX_CORE_TTT.FFF, where</p> <ul> <li>LLLL is the type of phospholipid</li> <li>AA stands for all atom (Coarse-grained data in a separate upload)</li> <li>CHOLXX stands for the cholesterol concentration (CHOL10 for 10 mol%)</li> <li>TTT is the temperature</li> <li>FFF is the tile type (see above)</li> </ul> <p>Note that topologies/index files are the same regardless of temperature, and hence their file names do not have the TTT section.</p> <p>[1] <strong>DOI: </strong>10.1021/jp101759q</p> <p>[2] <strong>DOI: </strong>10.1021/acs.jctc.5b00935</p> <p>[3] <strong>DOI: </strong>10.1016/j.softx.2015.06.001</p>
Atomistic simulations of cholesterol in asymmetric lipid bilayers with varying degrees of lipid chain unsaturation
<p>Asymmetric membranes consisting of DOPC, cholesterol, and a lipid with a varying level of unsaturation were simulated at 310 K. The DOPC leaflet consisted of 130 molecules, whereas the other leaflet consisted of either 125 DLiPC with 2 double bonds in both chains, 120 DAPC with 4 double bonds in both chains, or 115 DDPC with 6 double bonds in both chains. These numbers were adjusted to prevent membrane bending. All systems contained 28 molecules (10 mol%) of cholesterol. The CHARMM36 force field [1] was used and the membranes were generated using CHARMM-GUI [2].</p> <p>The simulations were run for 1 microsecond using the GROMACS simulation suite [3]. Simulation parameters are found in the common mdp file.</p> <p>The upload contains simulation inputs and outputs that allows the replication, extension, or analysis of the simulation data:</p> <ul> <li>Topology files (top) and molecular definitions (itp)</li> <li>Index files (ndx)</li> <li>A common run parameter file (mdp)</li> <li>A run input file (tpr)</li> <li>Trajectory file (xtc) written every 100 ps</li> <li>Energy file (edr)</li> <li>Log file (log)</li> <li>Final structure file (gro)</li> <li>Continue point file (cpt)</li> </ul> <p>The files are named DOPC_LLLL_AA_CHOLXX_TTT.FFF, where</p> <ul> <li>LLLL is the type of phospholipid paired with DOPC</li> <li>AA stands for all atom (Coarse-grained data in a separate upload)</li> <li>CHOLXX stands for the cholesterol concentration (CHOL10 for 10 mol%)</li> <li>TTT is the temperature</li> <li>FFF is the tile type (see above)</li> </ul> <p>[1] <strong>DOI: </strong>10.1021/jp101759q</p> <p>[2] <strong>DOI: </strong>10.1021/acs.jctc.5b00935</p> <p>[3] <strong>DOI: </strong>10.1016/j.softx.2015.06.001</p>
Data for paper: Atomistic simulations of grain boundary migration under recrystallisation conditions
<p>The archive contains the data used to produce the results for the paper: Atomistic simulations of grain boundary migration under recrystallisation conditions, by C.P.Race, submitted to the IOP journal Modelling and Simulation in Materials Science and Engineering</p> <p>The archive contains:</p> <p>1) Juypter Notebooks that load and analyse the data, producing the figures used in the publication<br> 2) An author pre-print of the paper, prior to amendments suggested by the referees<br> 3) Copies of the figures produced by the notebooks<br> 4) .txt files of the data used in the publication.<br> 5) A README file describing the contents</p>
Dataset to reproduce MD simulations described in "An atomistic view of the YiiP structural changes upon zinc(II) binding"
<p>Here are collected topologies, parameters, distance restraints, starting coordinates and trajectories for all the simulations reported in the manuscript entitled "An atomistic view of the YiiP structural changes upon zinc(II) binding" </p>
Raw data for: Sublytic gasdermin-D pores captured in atomistic molecular simulations
<p>This archive contains data and code related to "Sublytic gasdermin-D pores captured in atomistic molecular simulations" by Schaefer & Hummer. Included are molecular dynamics parameter files, initial structures after system equilibration, final structures after production, subsampled production trajectories, and python scripts used for analysis. </p> <p>Publication doi: https://doi.org/10.7554/eLife.81432<br> <br> Contact information:<br> Name: Stefan L. Schaefer<br> Institution: Department of Theoretical Biophysics, Max Planck Institute of Biophysics<br> Address: Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany<br> Email: stefan.schaefer@biophys.mpg.de</p>
MD simulation input files and results for ,,Atomistic MD simulations of n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids"
<p>Input files and trajectories of n-alkane/lipid systems used in the article: ,,Atomistic MD simulations of n-alkanes in a phospholipid bilayer: CHARMM36 versus Slipids".</p> <p>Equilibrated starting configurations were created using CHARMM36. Otherwise, filenames specifiy the force field used (C36 or SL), Temperature and system composition.</p> <p>.xtc trajectories were created using gmx trjconv with options -pbc nojump -dt 10. run2 equals simulations from 100-200ns, run3 equals 200-300ns. The first 100ns were excluded from the analysis and are not included in this dataset.</p> <p>Exemplary .mdp files have been included for both force-fields. Please refer to the manuscript for the force field sources and additional information.</p>
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations: Simulations Topology, Coordinate, Parameters, Input and Output files
<p>The simulation data for the article: Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations.</p> <p>ck_metad.tar.gz: Includes the topology files, coordinates files and gromacs parameter input file (.mdp) used for WT-MetaD-HREX simulations with different c(K+), which are newly added runs for resubmission. The corresponding script files and Plumed files are in GitHub.</p> <p>eq_mini.tar.gz: Includes the parameter files required for the equilibration and minimization protocol.</p> <p>standard_md.tar.gz: Includes the topology files and coordinate files for all systems built in the article. Also include the hbfix parameters file required on the MD run, and the MD script file.</p> <p>metad.tar.gz: Includes the topology files, coordinates files and gromacs parameter input file (.mdp) used for WT-MetaD-HREX simulations. The corresponding script files and Plumed files are in GitHub.</p> <p>metad*fe*.tar.gz: Plumed HILLS files and metad.bias data used for drawing the free energy landscapes.</p> <p>ions.tar.gz: Data used for Figure.3 in the manuscript</p> <p>si_data.tar.gz: All data used for SI figures.</p>
Data and code for "Efficient calculation of the lattice thermal conductivity by atomistic simulations with ab-initio accuracy"
<p>This data set contains data and code related to the publication "Efficient calculation of the lattice thermal conductivity by atomistic simulations with ab-initio accuracy".</p>
Atomistic simulations of a POPC / POPC+cholesterol membrane with different simulation parameters
<p>Atomistic</p>
Molecular dynamics simulation primer for: Introduction to atomistic modeling and simulation of biomolecular systems
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