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1. Molecular Dynamics Simulation of a Designed Cyclic Peptide Bound to CTLA4

   https://doi.org/10.5281/zenodo.7186684  

   Thakkar, Ravindra; Comer, Jeffrey (October 2022, RSC medicinal chemistry)

   This data set for the manuscript entitled "Computational Design of a Cyclic Peptide that Inhibits the CTLA4 Immune Checkpoint Pathway" includes all files needed to run and analyze the simulations of a designed cyclic peptide (Peptide 16) bound to CTLA4 in the putative most stable binding configuration, which is detailed in Figure 6 of the paper. These files include molecular model structure files (NAMD psf), force field parameter files (in CHARMM format), initial atomic coordinates (pdb format), NAMD configuration files, NAMD output including restart files (in binary NAMD format) and trajectories in dcd format (downsampled to 10 ns per frame). Analysis is controlled by shell scripts (Bash-compatible) that call VMD Tcl scripts. These scripts and their output are also included. Version: 1.0 Conventions Used in These Files =============================== Structure Files ---------------- - ctla4_P16_wat.psf (original NAMD (XPLOR?) format psf file including atom details (type, charge, mass), as well as definitions of bonds, angles, dihedrals, and impropers for each dipeptide.) - ctla4_P16.pdb (initial coordinates before equilibration) - repart_*.psf (same as the above psf files, but the masses of non-water hydrogen atoms have been repartitioned by VMD script repartitionMass.tcl) - rest*.pdb (same as the above pdb files, but atoms have been marked for restraints in NAMD. These files are generated by doPrep.sh, with restraints applied to different atoms.) Force Field Parameters ---------------------- CHARMM format parameter files: - par_all36m_prot.prm (CHARMM36m FF for proteins) - toppar_water_ions_prot.str (CHARMM water and ions with NBFIX parameters needed for protein and others commented out) Template NAMD Configuration Files --------------------------------- These contain the most commonly used simulation parameters. They are called by the other NAMD configuration files (which are in the namd/ subdirectory): - template_min.namd (minimization) - template_rest.namd (NPT equilibration with different parts of the protein restrained) - template_prod.namd (for the long production simulations) Minimization ------------- - namd/min_*.0.namd Restraints ------------- - namd/rest_*.0.namd (both CTLA4 binding site and peptide atoms are restrained) - namd/rest_*.1.namd (CA atoms of CTLA4 and all atoms of the peptide are restrained) - namd/rest_*.2.namd (all atoms of only the peptide are restrained) - namd/rest_*.3.namd (only CA atoms of only the peptide are restrained) - namd/rest_*.4.namd (no atoms are restrained) Production ------------- - namd/pro_*.{D,E,F}.0.namd Analysis ------------- - interaction.sh (Shell script for running analysis with VMD) - calcSeparationNearestAtom.tcl (Calculate the separation between two selections, taking the shortest distance between any pair of atoms spanning the two selections. Accounts for (orthogonal) periodic boundary conditions.) - useful.tcl (VMD Tcl script with a library of useful procs, used by the script above) - sep_*.dat (Output of the above analysis containing rows with two columns: time in nanoseconds and minimum distance in Å) Scripts ------- Files with the .sh extension can be found throughout. These usually provide the highest level control for submission of simulations and analysis. Look to these as a guide to what is happening. 

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2. The Absolute Age of NGC3021

   https://doi.org/10.5281/zenodo.10729300  

   Ying, Martin; Chaboyer, Brian; Du, Wenxin (January 2024, Zenodo)

   Differential reddening corrected HST ACS photometry, Monte Carlo Parameters and Monte Carlo isochrones used to estimate the absolute age of NGC3201. The columns in the NGC3201_fitstars_DRCR.dat  file are:x   = star x position on the master framey   = star y position on the master framev   = F606W VEGA magi    = F814W VEGA magvi  = V-I VEGAmag Detailed instruction to read MC parameters and MC isochrones can be found in the notebook: Instruction on reading NGC3201 isochrones.ipynb 

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3. COAWST model simulations of warm and cool nearshore rip-current plumes

   https://doi.org/10.5281/zenodo.4272080  

   Moulton, Melissa (January 2020, Zenodo)

   This archive contains COAWST model input, grids and initial conditions, and output used to produce the results in a submitted manuscript. The files are:</p> model_input.zip: input files for simulations presented in this paper   ocean_rip_current.in: ROMS ocean model input file   swan_rip_current.in: SWAN wave model input file (example with Hs=1m)   coupling_rip_current.in: model coupling file   rip_current.h: model header file    model_grids_forcing.zip: bathymetry and initial condition files      hbeach_grid_isbathy_2m.nc: ROMS bathymetry input file      hbeach_grid_isbathy_2m.bot: SWAN bathymetry input file      hbeach_grid_isbathy_2m.grd: SWAN grid input file      hbeach_init_isbathy_14_18_17.nc: Initial temperature, cool surf zone dT=-1C case      hbeach_init_isbathy_14_18_19.nc: Initial temperature, warm surf zone dT=+1C case      hbeach_init_isbathy_14_18_16.nc: Initial temperature, cool surf zone dT=-2C case      hbeach_init_isbathy_14_18_20.nc: Initial temperature, warm surf zone dT=+2C case      hbeach_init_isbathy_14_18_17p5.nc: Initial temperature, cool surf zone dT=-0.5C case      hbeach_init_isbathy_14_18_18p5.nc: Initial temperature, warm surf zone dT=+0.5C case</p> model_output files: model output used to produce the figures      netcdf files, zipped      variables included:           x_rho (cross-shore coordinate, m)           y_rho (alongshore coordinate, m)           z_rho (vertical coordinate, m)           ocean_time (time since initialization, s, output every 5 mins)           h (bathymetry, m)           temp (temperature, Celsius)           dye_02 (surfzone-released dye)           Hwave (wave height, m)           Dissip_break (wave dissipation W/m2)            ubar (cross-shore depth-average velocity, m/s, interpolated to rho-points)      Case_141817.nc: cool surf zone dT=-1C Hs=1m      Case_141819.nc: warm surf zone dT=+1C Hs=1m      Case_141816.nc: cool surf zone dT=-2C Hs=1m      Case_141820.nc: warm surf zone dT=-2C Hs=1m      Case_141817p5.nc: cool surf zone dT=-0.5C Hs=1m      Case_141818p5.nc: warm surf zone dT=+0.5C Hs=1m      Case_141817_Hp5.nc: cool surf zone dT=-1C Hs=0.5m      Case_141819_Hp5.nc: warm surf zone dT=+1C Hs=0.5m      Case_141817_Hp75.nc: cool surf zone dT=-1C Hs=0.75m      Case_141819_Hp75.nc: warm surf zone dT=+1C Hs=0.75m</p> COAWST is an open source code and can be download at https://coawstmodel-trac.sourcerepo.com/coawstmodel_COAWST/. Descriptions of the input and output files can be found in the manual distributed with the model code and in the glossary at the end of the ocean.in file.</p> Corresponding author: Melissa Moulton, mmoulton@uw.edu</p> 

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4. Simulation Data for Design of Peptides that Fold and Self-Assemble on Graphite

   https://doi.org/10.5281/zenodo.6426152  

   Comer, Jeffrey; Thakkar, Ravindra; Velásquez-Silva, Astrid; Miranda-Carvajal, Ingrid (January 2022, Zenodo)

   {"Abstract":["This data set for the manuscript entitled "Design of Peptides that Fold and Self-Assemble on Graphite" includes all files needed to run and analyze the simulations described in the this manuscript in the molecular dynamics software NAMD, as well as the output of the simulations. The files are organized into directories corresponding to the figures of the main text and supporting information. They include molecular model structure files (NAMD psf or Amber prmtop format), force field parameter files (in CHARMM format), initial atomic coordinates (pdb format), NAMD configuration files, Colvars configuration files, NAMD log files, and NAMD output including restart files (in binary NAMD format) and trajectories in dcd format (downsampled to 10 ns per frame). Analysis is controlled by shell scripts (Bash-compatible) that call VMD Tcl scripts or python scripts. These scripts and their output are also included.<\/p>\n\nVersion: 2.0<\/p>\n\nChanges versus version 1.0 are the addition of the free energy of folding, adsorption, and pairing calculations (Sim_Figure-7) and shifting of the figure numbers to accommodate this addition.<\/p>\n\n\nConventions Used in These Files\n===============================<\/p>\n\nStructure Files\n----------------\n- graph_*.psf or sol_*.psf (original NAMD (XPLOR?) format psf file including atom details (type, charge, mass), as well as definitions of bonds, angles, dihedrals, and impropers for each dipeptide.)<\/p>\n\n- graph_*.pdb or sol_*.pdb (initial coordinates before equilibration)\n- repart_*.psf (same as the above psf files, but the masses of non-water hydrogen atoms have been repartitioned by VMD script repartitionMass.tcl)\n- freeTop_*.pdb (same as the above pdb files, but the carbons of the lower graphene layer have been placed at a single z value and marked for restraints in NAMD)\n- amber_*.prmtop (combined topology and parameter files for Amber force field simulations)\n- repart_amber_*.prmtop (same as the above prmtop files, but the masses of non-water hydrogen atoms have been repartitioned by ParmEd)<\/p>\n\nForce Field Parameters\n----------------------\nCHARMM format parameter files:\n- par_all36m_prot.prm (CHARMM36m FF for proteins)\n- par_all36_cgenff_no_nbfix.prm (CGenFF v4.4 for graphene) The NBFIX parameters are commented out since they are only needed for aromatic halogens and we use only the CG2R61 type for graphene.\n- toppar_water_ions_prot_cgenff.str (CHARMM water and ions with NBFIX parameters needed for protein and CGenFF included and others commented out)<\/p>\n\nTemplate NAMD Configuration Files\n---------------------------------\nThese contain the most commonly used simulation parameters. They are called by the other NAMD configuration files (which are in the namd/ subdirectory):\n- template_min.namd (minimization)\n- template_eq.namd (NPT equilibration with lower graphene fixed)\n- template_abf.namd (for adaptive biasing force)<\/p>\n\nMinimization\n-------------\n- namd/min_*.0.namd<\/p>\n\nEquilibration\n-------------\n- namd/eq_*.0.namd<\/p>\n\nAdaptive biasing force calculations\n-----------------------------------\n- namd/eabfZRest7_graph_chp1404.0.namd\n- namd/eabfZRest7_graph_chp1404.1.namd (continuation of eabfZRest7_graph_chp1404.0.namd)<\/p>\n\nLog Files\n---------\nFor each NAMD configuration file given in the last two sections, there is a log file with the same prefix, which gives the text output of NAMD. For instance, the output of namd/eabfZRest7_graph_chp1404.0.namd is eabfZRest7_graph_chp1404.0.log.<\/p>\n\nSimulation Output\n-----------------\nThe simulation output files (which match the names of the NAMD configuration files) are in the output/ directory. Files with the extensions .coor, .vel, and .xsc are coordinates in NAMD binary format, velocities in NAMD binary format, and extended system information (including cell size) in text format. Files with the extension .dcd give the trajectory of the atomic coorinates over time (and also include system cell information). Due to storage limitations, large DCD files have been omitted or replaced with new DCD files having the prefix stride50_ including only every 50 frames. The time between frames in these files is 50 * 50000 steps/frame * 4 fs/step = 10 ns. The system cell trajectory is also included for the NPT runs are output/eq_*.xst.<\/p>\n\nScripts\n-------\nFiles with the .sh extension can be found throughout. These usually provide the highest level control for submission of simulations and analysis. Look to these as a guide to what is happening. If there are scripts with step1_*.sh and step2_*.sh, they are intended to be run in order, with step1_*.sh first.<\/p>\n\n\nCONTENTS\n========<\/p>\n\nThe directory contents are as follows. The directories Sim_Figure-1 and Sim_Figure-8 include README.txt files that describe the files and naming conventions used throughout this data set.<\/p>\n\nSim_Figure-1: Simulations of N-acetylated C-amidated amino acids (Ac-X-NHMe) at the graphite\u2013water interface.<\/p>\n\nSim_Figure-2: Simulations of different peptide designs (including acyclic, disulfide cyclized, and N-to-C cyclized) at the graphite\u2013water interface.<\/p>\n\nSim_Figure-3: MM-GBSA calculations of different peptide sequences for a folded conformation and 5 misfolded/unfolded conformations.<\/p>\n\nSim_Figure-4: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite\u2013water interface at 370 K.<\/p>\n\nSim_Figure-5: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite\u2013water interface at 295 K.<\/p>\n\nSim_Figure-5_replica: Temperature replica exchange molecular dynamics simulations for the peptide cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) with 20 replicas for temperatures from 295 to 454 K.<\/p>\n\nSim_Figure-6: Simulation of the peptide molecule cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) in free solution (no graphite).<\/p>\n\nSim_Figure-7: Free energy calculations for folding, adsorption, and pairing for the peptide CHP1404 (sequence: cyc(GTGSGTG-GPGG-GCGTGTG-SGPG)). For folding, we calculate the PMF as function of RMSD by replica-exchange umbrella sampling (in the subdirectory Folding_CHP1404_Graphene/). We make the same calculation in solution, which required 3 seperate replica-exchange umbrella sampling calculations (in the subdirectory Folding_CHP1404_Solution/). Both PMF of RMSD calculations for the scrambled peptide are in Folding_scram1404/. For adsorption, calculation of the PMF for the orientational restraints and the calculation of the PMF along z (the distance between the graphene sheet and the center of mass of the peptide) are in Adsorption_CHP1404/ and Adsorption_scram1404/. The actual calculation of the free energy is done by a shell script ("doRestraintEnergyError.sh") in the 1_free_energy/ subsubdirectory. Processing of the PMFs must be done first in the 0_pmf/ subsubdirectory. Finally, files for free energy calculations of pair formation for CHP1404 are found in the Pair/ subdirectory.<\/p>\n\nSim_Figure-8: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) where the peptides are far above the graphene\u2013water interface in the initial configuration.<\/p>\n\nSim_Figure-9: Two replicates of a simulation of nine peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite\u2013water interface at 370 K.<\/p>\n\nSim_Figure-9_scrambled: Two replicates of a simulation of nine peptide molecules with the control sequence cyc(GGTPTTGGGGGGSGGPSGTGGC) at the graphite\u2013water interface at 370 K.<\/p>\n\nSim_Figure-10: Adaptive biasing for calculation of the free energy of the folded peptide as a function of the angle between its long axis and the zigzag directions of the underlying graphene sheet.<\/p>\n\n <\/p>"],"Other":["This material is based upon work supported by the US National Science Foundation under grant no. DMR-1945589. A majority of the computing for this project was performed on the Beocat Research Cluster at Kansas State University, which is funded in part by NSF grants CHE-1726332, CNS-1006860, EPS-1006860, and EPS-0919443. This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number ACI-1548562, through allocation BIO200030."]} 

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5. New Hampshire Soil Sensor Network: Air Temperature, Soil Temperature, Soil Water Content, and Soil Electrical Conductivity, 2012 - ongoing

   https://doi.org/10.6073/pasta/9f31b023820f207979e9c07275d0a84e  

   Contosta, Alexandra R; Frey, Serita D; Perry, Apryl (January 2024, Environmental Data Initiative)

   The goal of the New Hampshire Soil Sensor Network is to examine spatial and temporal changes in soil properties and processes as the climate changes. Data collected can also calibrate and validate models that examine how ecosystems may respond to changing climate and land use. To determine how soil processes are affected by climate change and land management, this soil sensor network measures snow depth, air temperature, soil temperature, soil volumetric water content, and soil electrical conductivity, as well as soil CO2 fluxes. This data package includes data from the air temperature, soil temperature, soil volumetric water content, and electrical conductivity sensors. Data were collected at the following sites: BRT = Bartlett Experimental Forest, Bartlett, NH; BDF = Burley-Demmerit Farm, Lee, NH; DCF = Dowst Cate Forest, Deerfield, NH; HUB = Hubbard Brook Experimental Forest, Woodstock, NH; SBM = Saddleback Mountain, Deerfield, NH; THF = Thompson Farm, Durham, NH; and Trout Pond Brook, Strafford, NH. 

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