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Dataset results
119 results for “Gromacs”
POPC/Cholesterol (50:50) lipid membrane, 303K, Charmm36 force field from charmm-gui, simulation files and 200 ns trajectory for Gromacs MD simulation engine v5.1.2
<p>The starting structure was obtained from CHARMM-GUI Membrane Builder v1.7 (http://www.charmm-gui.org/) online tool. [1]</p> <p>All runs were performed with Gromacs 5.1.2 software package and CHARMM36 additive force field parameters obtained from CHARMM-GUI input files [1]. Conditions: T=303, 80 POPC and 80 Cholesterol molecules, 7200 tip3p waters, 200ns trajectory (preceded with equilibration)</p> <p>These data were originally obtained for the nmrlipids.blospot.fi project.</p> <p>Find more details at nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi</p> <p>[1] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field, J. Lee et al.<strong>,</strong> JCTC,<strong> </strong>DOI: 10.1021/acs.jctc.5b00935</p>
POPC/Cholesterol (70:30) lipid membrane, 303K, Charmm36 force field, simulation files and 200 ns trajectory for Gromacs MD simulation engine v5.1.2
<p>The starting structure was obtained from CHARMM-GUI Membrane Builder v1.7 (http://www.charmm-gui.org/) online tool. [1]</p> <p>All runs were performed with Gromacs 5.1.2 software package and CHARMM36 additive force field parameters obtained from CHARMM-GUI input files [1]. Conditions: T=303, 128 POPC molecules, 5120 tip3p waters, 200ns trajectory (preceded with equilibration)</p> <p>These data were originally obtained for the nmrlipids.blospot.fi project.</p> <p>Find more details at nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi</p> <p>[1] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field, J. Lee et al.<strong>,</strong> JCTC,<strong> </strong>DOI: 10.1021/acs.jctc.5b00935</p>
POPC/Cholesterol (70:30) lipid membrane, 303K, Charmm36 force field through the use of Gromacs input files, simulation files and 100 ns trajectory for openMM simulation engine v7
<p>The starting structure was obtained from CHARMM-GUI Membrane Builder v1.7 (http://www.charmm-gui.org/) online tool. [1]</p> <p>All runs were performed with openMM simulation engine v7 and CHARMM36 additive force field parameters obtained from CHARMM-GUI input files [1]. Specifically, Gromacs file format provided by [1] was specifically used for this simulation.</p> <p>Conditions: T=303, 84 POPC and 36 Cholesterol molecules, 4800 tip3p waters, 100ns trajectory (preceded with equilibration).</p> <p>These data were originally obtained for the nmrlipids.blospot.fi project.</p> <p>Find more details at nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi</p> <p>[1] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field, J. Lee et al.<strong>,</strong> JCTC,<strong> </strong>DOI: 10.1021/acs.jctc.5b00935</p>
MD simulation trajectory of a lipid bilayer: Pure POPC in water. SLIPIDS, Gromacs 4.6.3. 2016.
<p>MD simulation trajectory files, for fully hydrated POPC bilayer [512 POPC, 23943 WAT]. The SLIPIDS force field was used with Gromacs 4.6.3. Conditions: T=298K. 170 ns each trajectory, last 100 ns analyzed.</p>
POPC/Cholesterol (50:50) lipid membrane, 303K, Charmm36 force field, simulation files and 100 ns trajectory for GROMACS simulation engine v5
<p>All runs were performed with GROMACS simulation engine v5 and CHARMM36 additive force field parameters obtained from MacKerell lab website (http://mackerell.umaryland.edu/charmm_ff.shtml, also available at</p> <p>https://doi.org/10.5281/zenodo.209080). Conditions: T=303, 80 POPC and 80 Cholesterol molecules, 7200 tip3p waters, 100ns trajectory (preceded with equilibration). </p> <p>These data were originally obtained for the nmrlipids.blospot.fi project.</p> <p>Find more details at nmrlipids.blospot.fi and https://github.com/NMRLipids/nmrlipids.blogspot.fi</p>
MD simulation trajectory of a fully hydrated DPPG bilayer @298K: SLIPIDS, Gromacs 5.0.4. 2017.
<p>MD simulation trajectory files, for fully hydrated DPPG bilayer [288 DPPG, 11232 WAT and 288 NA ions]. The SLIPIDS force field was used with Gromacs 5.0.4. Conditions: T=298K. 400 ns trajectory, last 100 ns uploaded for analysis.</p>
MD simulation trajectory of a fully hydrated POPG bilayer: SLIPIDS, Gromacs 5.0.4. 2017.
<p>MD simulation trajectory files, for fully hydrated POPG bilayer [288 POPG, 10664 WAT and 288 NA ions]. The SLIPIDS force field was used with Gromacs 5.0.4. Conditions: T=298K. 250 ns trajectory, last 100 ns uploaded for analysis.</p>
MD simulation trajectory of a fully hydrated DPPE bilayer: SLIPIDS, Gromacs 5.0.4. 2017.
<p>MD simulation trajectory files, for fully hydrated DPPE bilayer [288 DPPE, 9386 WAT]. The SLIPIDS force field was used with Gromacs 5.0.4. Conditions: T=336K. 200 ns trajectory, last 100 ns uploaded for analysis.</p>
MD simulation trajectory of a fully hydrated DPPG bilayer @314K: SLIPIDS, Gromacs 5.0.4. 2017.
<p>MD simulation trajectory files, for fully hydrated DPPG bilayer [288 DPPG, 11232 WAT and 288 NA ions]. The SLIPIDS force field was used with Gromacs 5.0.4. Conditions: T=314K. 200 ns trajectory, last 100 ns uploaded for analysis.</p>
MD simulation trajectory of a fully hydrated DOPS bilayer: SLIPIDS, Gromacs 5.0.4. 2017.
<p>MD simulation trajectory files, for fully hydrated DOPS bilayer [288 DOPS, 11232 WAT and 288 NA ions]. The SLIPIDS force field was used with Gromacs 5.0.4. Conditions: T=303K. 200 ns trajectory, last 100 ns uploaded for analysis.</p>
Molecular dynamics trajectories, GROMACS input files, and analysis code from "Rational optimization of a transcription factor activation domain inhibitor" by Basu et. al, Nature Structural & Molecular Biology, 2023
<p>Molecular dynamics trajectories, GROMACS input files, and analysis code from "Rational optimization of a transcription factor activation domain inhibitor" by Basu et. al, Nature Structural & Molecular Biology, 2023</p> <p> </p> <p> </p>
Amyloid-beta 16-22 peptide monomer simulation (150 mM NaCl) with the CHARMM36m force field and Gromacs (Run 3)
<p>MD simulations of the Amyloid-beta 16-22 monomer at 150 mM NaCl concentration with CHARMM36m force field and Gromacs. This repository contains the third out of three independent runs. </p> <p>Files belong to the publication "<a href="https://doi.org/10.1021/acs.jcim.0c01063">https://doi.org/10.1021/acs.jcim.0c01063</a>"</p> <p>All the simulation parameters and force field files are uploaded into this repository. Simulations are done with Gromacs 2018.3</p> <p>Total simulation time is 500 ns. Frames are saved with 100 ps frequency. </p>
Simulations DSPC bilayers (512 lipids) using charmm36 ff in gromacs
<p>Collection simulations of DSPC (512 lipids) bilayers in gromacs using the charmm36 force field. Temperatures of 333 and 338 K are included. The list of systems can be found below:</p> <p>1) DSPC_512_NaCl_150mM_333K (620ns)<br> 2) DSPC_512_NaCl_150mM_338K (500ns)</p> <p>For further information read the Readme file provided for each simulation.</p>
Simulations DPPC bilayers (512 lipids) using charmm36 ff in gromacs
<p>Collection simulations of DPPC (512 lipids) bilayers in gromacs using the charmm36 force field. Several temperatures between 315 and 338 K are included. The list of systems can be found below where the several parameter are:</p> <p>1) DPPC_512_NaCl_150mM_315K_v-rescale (500ns)<br> 2) DPPC_512_NaCl_150mM_320K (700ns)<br> 3) DPPC_512_NaCl_150mM_320K_v-rescale (500ns)<br> 4) DPPC_512_NaCl_150mM_322K_v-rescale (700ns)<br> 5) DPPC_512_NaCl_150mM_325K (500ns)<br> 6) DPPC_512_NaCl_150mM_325K_v-rescale (500ns)<br> 7) DPPC_512_NaCl_150mM_325K_cutoff09 (500ns)<br> 8) DPPC_512_NaCl_150mM_325K_MEMB_338K (500ns)<br> 9) DPPC_512_NaCl_150mM_338K (500ns)</p> <p>For further information read the Readme file provided for each simulation.</p>
Set simulations small pure bilayers (72 lipids) using charmm36 ff in gromacs (DPPC, POPC)
<p>Collection simulations of DPPC and POPC bilayers in gromacs using the charmm36 force field. The list of systems describing their particular simulation conditions can be found below:</p> <p>1) DPPC_72_325K (500ns)<br> 2) DPPC_72_310K_rmcomm_leaflets (500ns)<br> 3) DPPC_72_310K_rmcomm_leaflets_low_hydration (500ns)<br> 4) POPC_72_310K (500ns)<br> 5) POPC_72_310K_rmcomm_leaflets (500ns)<br> 6) POPC_72_310K_rmcomm_leaflets_low_hydration (550ns)<br> 7) POPC_72_303K_rmcomm_leaflets_low_hydration (550ns)</p> <p>For further information read the Readme file provided for each simulation.</p>
Progeny Project Gromacs MD Simulations of the MW8 surfactant
<p>"MW8" thiophene based surfactant molecule at the water-vacuum interface, data from the PROGENY project ,<br> gromacs 2021.2 input and output.<br> From the trajectories contained in this archive density profiles and surface tensions can be extracted.</p> <p>Different number of molecules per surface in each sub directory. See README.txt.</p>
Progeny Project Gromacs input and trajectories of a C12E6 surfactant model at the vacuum-water interface
<p>This is gromacs 2021.2 input and output for an all-atom C12E6 surfactant molecule at the water-vacuum<br> interface with TIP4P-ew and SPC/E water models.</p>
Lysozyme-in-water 1us full-atom GROMACS simulation for MDAnalysis parallelization benchmark
<p>I'm using trajectory and topology for an 1us run generated according to <a href="http://www.mdtutorials.com/gmx/lysozyme/index.html">lysozyme in water</a> tutorial and used later in <a href="https://www.nature.com/articles/s41598-023-32459-x">this</a> publication (charged HIS trajectory).</p> <p>A full-atom <code>xtc</code> trajectory containing 25690 atoms in total (see topology for more detail).</p> <p>Associated benchmark and its description can be found <a href="https://gist.github.com/marinegor/17558d1685cd2f24a6de65aa99cf5c9e">here</a>.</p>
Introduction to HPC: molecular dynamics simulations with GROMACS: log files
<p>Introduction to HPC: molecular dynamics simulations with GROMACS: log files corresponding to the exercises 1.X 2.X 3.X</p>
Introduction to HPC: molecular dynamics simulations with GROMACS: output files - Devana
<p> Introduction to HPC: molecular dynamics simulations with GROMACS: log files corresponding to the exercises 1.1, 1.2 2.1 3.1 and 3.2</p>
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