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220 results for “force field”
GMX_lipid17.ff: Gromacs Port of the amber LIPID17 force field
<p>This is a Gromacs port of the amber LIPID17 force field. To use this force field, the user can construct the lipid bilayer using Charmm-GUI and convert the atom names to the amber atom names using charmmlipid2amber.py. This port has also retained the modular feature of the LIPID17 force field, where the user can customise the head group or acryl chain and use pdb2gmx to construct the topology.</p> <p>The coordinate files for the amber lipids can also be obtained from the `gro` folder. The force field `lipid17.ff`, itp file `lipid17.itp` and a custom PI head group are all included in the attached compressed file. For the details of the generation and validation protocol, please consult the relevant <a href="https://github.com/xiki-tempula/gmx_lipid17.ff">Github</a> page.</p>
Input files for simulation of potassium channels using the AMOEBA polarizable force field
<p>This dataset contains input Tinker xyz and key files for the simulation of KcsA potassium channels in DOPC bilayer, a simple script for converting CHARMM pdb file to Tinker xyz file, and modified Tinker source code to support one-dimensional position restraints.<br> "params.tar.gz" contains a description of the force field modifications.<br> <br> To use "mod2", add the following lines to the key file.</p> <pre><code>#compatible with amoebabio18.prm polarize 5 1.4500 0.3900 3 polarize 11 1.4500 0.3900 9 polarize 3 1.7500 0.3900 1 5 7 50 225 227 polarize 9 1.7500 0.3900 1 7 11 50 225 227</code></pre> <p> </p>
GAP-20 machine learning force field for phosphorus
<p>This dataset contains the force-field parameter files and reference database described in the manuscript "A general-purpose machine-learning force field for bulk and nanostructured phosphorus" (to be published).</p>
Output from the Glacier Energy and Mass Balance (GEMB v1.0) forced with 3-hourly ERA5 fields and gridded to 10km, Greenland and Antarctica 1979-2024
<p>These model output of firn air content (FAC) and surface mass balance (SMB) are from version 1.0 of the open-source Glacier Energy and Mass Balance model. GEMB is a column model of ice sheet and glacier surface-atmospheric energy and mass exchange as well as firn state. GEMB has been integrated into the open-source Ice-Sheet and Sea-level System Model which can be downloaded at https://issm.jpl.nasa.gov/. Here, GEMB is forced with 3-hourly ERA5 output from 1979 through end of 2024. For Greenland and its periphery, the ERA5 surface temperature and downwelling longwave radiation forcing are spatially bias-corrected for each month. All values are adjusted by the difference between the RACMO2.3 and the ERA5 1980-2015 monthly means. The GEMB output is bilinearly interpolated onto a 10km grid, from the native ISSM grid, and the output is given as 5-day output or as monthly.</p>
Automatic learning of hydrogen-bond fixes in an AMBER RNA force field - dataset
<p>Supporting data related to manuscript "Automatic learning of hydrogen-bond fixes in an AMBER RNA force field"</p>
Slipids Force Field v2.0 (2016)
<p>Slipids force field: files for Gromacs<br> -----------------------------------------------------------</p> <p>Authors: Joakim Jämbeck, Inna Ermilova, Alexander Lyubartsev<br> Department of Materials and Environmental Chemistry,<br> Stockholm University, Stockholm 10691 Sweden<br> e-mail: alexander.lyubartsev@mmk.su.se</p> <p>Content:</p> <p>SLipids_FF: directory containing the force field. Included into the Gromacs<br> topology file by: <br> #include "SLipids_FF/forcefield.itp"</p> <p>itp_files: itp files for various lipids</p> <p> </p> <p>The force field can be used together with the AMBER99SB/AMBER03/GAFF<br> for proteins</p> <p><br> !!!! MAKE SURE YOU CITE THE FOLLOWING REFERENCES WHEN USING THIS FORCE FIELD !</p> <p><br> Saturated PC lipids:</p> <p>Joakim P. M. Jämbeck and Alexander P. Lyubertsev, "Derivation and Systematic<br> Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids",<br> J. Phys. Chem. B, 2012, 116, 3164-3179 (2012) DOI: 10.1021/jp212503e</p> <p>POPC, DOPC, SOPC, DOPE, POPE and similar:<br> <br> Joakim P. M. Jämbeck and Alexander P. Lyubertsev, "An Extension and Further<br> Validation of an All-Atomistic Force Field for Biological Membranes"<br> J. Chem. Theory Comput., 8, 2938-2948, (2012) DOI: 10.1021/ct300342n</p> <p>PS, PG, SM lipids and Cholesterol:</p> <p>Joakim P. M. Jämbeck and Alexander P. Lyubertsev, "Another Piece of the<br> Membrane Puzzle: Extending Slipids Further"<br> J. Chem. Theory Comput., 9 (1), 774-784 (2013) DOI: 10.1021/ct300777p</p> <p>Polyinsaturated lipids:</p> <p>Inna Ermilova and Alexander Lyubartsev:, "Extension of the Slipids Force<br> Field for Polyunsaturated Lipids",<br> J. Phys. Chem. B, 120 (50), 12826–12842 (2016)</p> <p><br> Cite also this paper on Charmm36 force field since bond and angle parameters,<br> as well as a part of Lennard-Jones parameters and torsion angles in the lipid<br> headgroups in SLipids are taken from the Charmm36 force field:</p> <p>Jeffery B. Klauda, Richard M. Venable, Alfredo Freites, Joseph W. O’Connor,<br> Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D.<br> MacKerell, Jr. and Richard W. Pastor, "Update of the CHARMM all-atom additive<br> force field for lipids: Validation on six lipid types", J.Phys.Chem B, 114,<br> 7830–78 (2010)</p> <p> </p>
Input files for "Faster Simulations with a 5 fs Time Step for Lipids in the CHARMM Force Field"
<p>The performance of all-atom molecular dynamics simulations is limited by an integration time step of 2 fs, which is needed to resolve the fastest degrees of freedom in the system, namely, the vibration of bonds and angles involving hydrogen atoms. The virtual interaction sites (VIS) method replaces hydrogen atoms by massless virtual interaction sites to eliminate these degrees of freedom while keeping intact nonbonded interactions and the explicit treatment of hydrogen atoms. We have modified the existing VIS algorithm for most lipids in the popular CHARMM36 force field by increasing the hydrogen atom masses at regular intervals in the lipid acyl chains and obtained lipid properties and pore formation free energies in very good agreement with those calculated in simulations without VIS. Our modified VIS scheme enables a 5 fs time step resulting in a significant performance gain for all-atom simulations of membranes. The method has the potential to make longer time and length scales accessible in all-atom simulations of membrane–protein complexes.</p> <p>The file set contains individual lipid topologies for virtual interaction sites for standard CHARMM lipids, as well as a README file with instructions on how to implement the VIS algorithm for membranes or membrane-protein complexes</p> <p>Please Cite: <a href="//pubs.acs.org/doi/10.1021/acs.jctc.8b00267">10.1021/acs.jctc.8b00267</a></p> <p> </p>
Supporting Information for "An empirical modification of the force field approach to describe the modulation of galactic cosmic rays close to Earth in a broad range of rigidities"
<p>This supporting information provides the Data Set S1 used to produce Fig. 6 in <strong>"An empirical modification of the force field approach to describe the modulation of galactic cosmic rays close to Earth in a broad range of rigidities"</strong> (Gieseler et al., 2017). It can be used to calculate the rigidity-dependent solar modulation potential <span class="math-tex">\(\phi(P)\)</span> for monthly intervals from 1973-2017 following Eq. 10 in Gieseler et al. (2017).</p> <p>If you use this data, please refer to and cite <strong>BOTH</strong> following publications:</p> <ul> <li>Gieseler, J., B. Heber, and K. Herbst, <em>An empirical modification of the force field approach to describe the modulation of galactic cosmic rays close to Earth in a broad range of rigidities</em>, J. Geophys. Res., 2017 (doi:10.1002/2017JA024763).</li> <li>Usoskin, I. G., G. A. Bazilevskaya, and G. A. Kovaltsov, <em>Solar modulation parameter for cosmic rays since 1936 reconstructed from ground-based neutron monitors and ionization chambers</em>, J. Geophys. Res., 2011 (doi:10.1029/2010JA016105).</li> </ul> <p>This data set contains the solar modulation potential values in MV for monthly intervals from 1973-2017 derived from the proton proxies IMP-8 He and ACE/CRIS C (Phi_pp), and from Usoskin et al. (2011) as provided by http://cosmicrays.oulu.fi/phi/phi.html (Phi_Uso11). The uncertainties of Phi_pp are given in column 4, those of Phi_Uso11 are 26 MV for the observed period. The LIS used to calculate the modulation potentials is that from Burger et al. (2000) as given by Usoskin et al. (2005).</p> <p>Column 1: Fractional year (start of interval)<br> Column 2: Month<br> Column 3: Phi_pp /MV<br> Column 4: Uncertainty of Phi_pp /MV<br> Column 5: Phi_Uso11 /MV</p> <p>Data also available at http://www.ieap.uni-kiel.de/et/ag-heber/cosmicrays</p>
CHARMM36M Force Field Parameters for the Thioester Bond between Cysteine and Glycine
<p>CHARMM36M force field parameters for the thioester bond connecting the side chain of a cysteine to the carbonyl of a C-terminal glycine.</p> <p>The dataset includes parameter and auxiliary files in GROMACS format. In addition, a short tutorial shows how to patch the CHARMM36M force field and use the parameters.</p> <p>These parameters have been developed for the parameterization and simulation of the Ubc6 ubiquitin complex, but can be used with any conparable system.</p> <p>Details about the parameterization are provided in:</p> <p><br><a href="https://www.embopress.org/doi/full/10.1038/s44318-024-00301-3">Swarnkar, Anuruti, Florian Leidner, Ashok K. Rout, Sofia Ainatzi, Claudia C. Schmidt, Stefan Becker, Henning Urlaub, Christian Griesinger, Helmut Grubmüller, and Alexander Stein. "Determinants of chemoselectivity in ubiquitination by the J2 family of ubiquitin-conjugating enzymes." <em>The EMBO Journal</em> (2024): 1-35.</a></p> <p> </p> <p> </p>
TUK-FFDat - Data scheme and data format for transferable force fields for molecular simulation
<p>Online repository to suplement the following publication:</p> <p>G. Kanagalingam, S. Schmitt, F. Fleckenstein, S. Stephan: Data scheme and data format for transferable force fields for molecular simulation, Scientific Data, accepted (2023).</p>
Data deposit accompanying Accurate Energy Barriers for Catalytic Reaction Pathways: An Automatic Training Protocol for Machine Learning Force Fields
<p>Dataset accompanying the paper: <em>"Accurate Energy Barriers for Catalytic Reaction Pathways: An Automatic Training Protocol for Machine Learning Force Fields"</em>. Contains the training sets curated during active learning as well as .xyz files used for creating the Figures. <br> <br> The paper highlights that the computational efficiency of ML force fields not only results in decreased computational costs for routine catalytic investigations but also facilitates more comprehensive exploration of catalytic pathways.</p> <p><strong>Published in NPJ Computational Materials</strong>: <a href="https://www.nature.com/articles/s41524-023-01124-2">https://www.nature.com/articles/s41524-023-01124-2</a><br> Formerly on Arxiv: <a href="https://arxiv.org/abs/2301.09931">https://arxiv.org/abs/2301.09931</a></p>
Pure POPC Membrane Simulation Using Charmm-Drude Force Field with OpenMM
<p>400 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 72 POPC lipids and 2809 SWM4 water molecules.</p> <p>The simulation have been performed using OpenMM 7.4.1</p> <p>Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset.</p> <p>This dataset does not contain the water molecules.</p> <p><strong>Please note that</strong> the trajectories might need to be realigned.</p>
Simulation files for POPC lipid membrane with Slipids-VIS force field for Gromacs MD simulation engine
<p>The tar.gz archive contains simulation input files that were used in the publication Transmembrane potential modeling: Comparison between methods of constant electric field and ion imbalance.</p> <p>http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b01202</p> <p>The files are meant to be used with <strong>Gromacs</strong> simulation package (gromacs.org).</p> <p>A modified Slipids force field, <strong>Slipids-VIS</strong>, is introduced. It uses Virtual Interaction sites in order to speed up simulation. The technique is described in the aforementioned work. The archive contains working topology for <strong>POPC</strong> lipid molecules and 6fs timestep without any significant loss of accuracy.</p>
Supplementary underlying data for "Evaluating parameterization protocols for hydration free energy calculations with the AMOEBA polarizable force field"
<p>This dataset includes additional underlying data for the publication "Evaluating parameterization protocols for hydration free energy calculations with the AMOEBA polarizable force field"</p> <p>Contents:</p> <p>Tukey Honest Significant Difference (HSD) results for solutes 1-47 across all seven parameter sets, as *.txt. These are pairwise comparisons of results between all possible parameter sets. Significant differences are treated as p < 0.05.</p>
MD Simulation of AtALMT9 TMD Using Martini3 and charmm36 Force Field
<p>This dataset contains the MD simulation data associated with the article:</p> <p>"Structural basis for malate-driven, pore lipid-regulated activation of the Arabidopsis vacuolar anion channel ALMT9"</p> <p><em>(Not published yet)</em></p> <p> </p> <p>Folder</p> <p>AA : All-atom simulation files.</p> <p>CG : Coarse-grained simulation files.</p> <p>toppar : parameter files.</p> <p> </p> <p>File Description</p> <p>conf.pdb : Initial structure of the simulation.</p> <p>all.fit.10ns.now.zen.xtc : trajectory file without water. </p> <p>now.pdb : coordinate file of corresponding trajectory.</p> <p>topol.top : GROMACS topology file.</p> <p> </p> <p> </p>
Molecular dynamics simulations of an Ago2-RNA complex in different force fields
<p>This set of simulations contains 2us of Ago2-RNA complex in Amber ff14SB + OL3, ff19SB + OL3 and Desmond OPLS4 force fields. The polarizable force field AMOEBA has two simulation sets of 10*10ns and 2*100ns. The trajectories have been wrapped in the periodic box, centered around the protein atoms and the water molecules have been stripped out to conserve space using cpptraj. The trajectories are presented in Gromacs xtc-format which can be opened with the corresponding pdb file in multiple software tools such as VMD, PyMol or CaverAnalyst. The simulations are based on the crystal structure PDB ID 4W5O, where the missing loops were modeled using the Schrödinger Suite and missing nucleotides added manually. </p>
MD simulations of bOG:DMPC in CHARMM36 force field
<p>CHARMM-GUI based series of simulations of beta-octyl-D-glucopyranoside (b-OG) mixed with DMPC at different dilutions. bOG:DMPC mol ratios are 1:1, 1:2, and 2:3. The only change in the force field was changing atom names from 2H2 to H2 in BOG residue to allow **gmx grompp** to recognize protons as protons when setting up constraints for bonds with hydrogens.</p> <p>Simulations are performed in highly hydrated state. I can name it "more than 50 water per two acyl chains"; "water per lipid" measure doesn't work here because bOG has just a single hydrocarbon tail.</p> <p>Trajectory length: 500 ns (20 ps step). T = 303 K. </p> <p>In this version we add *znd files where atom names are unique (changed in a new version of BOG.itp).</p>
Pure POPC Membrane with 1000mM NaCl simulations using Drude Polarizable Force Field and OpenMM
<p>500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 115 NaCl, and 6400 SWM4 water molecules.</p> <p>The simulation have been performed using OpenMM 7.4.1</p> <p>Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset.</p> <p>wrapped.dcd has a frame saving frequency of 100 ps.</p> <p><strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p><strong>This simulation consists of 5 sub-trajectories, each of which starts from the last frame of the previous one and runs for 100 ns. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong></p>
Pure POPC Membrane with 450mM NaCl simulations using Drude Polarizable Force Field and OpenMM
<p>500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 51 NaCl, and 6400 SWM4 water molecules.</p> <p>The simulation have been performed using OpenMM 7.4.1</p> <p>Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset.</p> <p>wrapped.dcd has a frame saving frequency of 100 ps.</p> <p><strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p><strong>This simulation consists of 5 sub-trajectories, each of which starts from the last frame of the previous one and runs for 100 ns. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong></p>
Pure POPC Membrane with 650mM CaCl2 simulations using Drude Polarizable Force Field and OpenMM
<p>500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 76 CaCl2, and 6400 SWM4 water molecules.</p> <p>The simulation have been performed using OpenMM 7.4.1</p> <p>Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset.</p> <p>wrapped.dcd has a frame saving frequency of 100 ps.</p> <p>The initial structures have been obtained from CHARMM-GUI.</p> <p> </p> <p><strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p><strong>This simulation consists of 5 sub-trajectories, each of which starts from the last frame of the previous one and runs for 100 ns. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong></p>
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