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1. 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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2. De novo design of a stapled peptide targeting SARS-CoV-2 spike protein receptor-binding domain

   https://doi.org/10.5281/zenodo.7844171  

   Thakkar, Ravindra; Comer, Jeffrey (April 2023, RSC medicinal chemistry)

   The dataset provided for the manuscript entitled "De novo design of a stapled peptide targeting SARS-CoV-2 spike protein receptor-binding domain" encompasses all the required files to execute and analyze simulations of a designed stapled peptide (Pep 39) attached to spike protein receptor binding domain in the most stable binding configuration, illustrated in Figure 3 of the paper. The dataset is composed of molecular model structure files in NAMD psf format, force field parameter files in CHARMM format, initial atomic coordinates in PDB format, NAMD configuration files, NAMD output files (which consist of restart files in binary NAMD format), and trajectories in dcd format (downsampled to 10 ns per frame). To manage the analysis, there are shell scripts (that work with Bash) that invoke VMD Tcl scripts. These scripts and their output are also contained in the dataset. 

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3. Simulation Files for Organic Contaminants and Atmospheric Nitrogen at the Graphene–Water Interface

   https://doi.org/10.5281/zenodo.6050816  

   Thakkar, Ravindra; Sandun, Gajaweera; Comer, Jeffrey (January 2022, Zenodo)

   {"Abstract":["This data set provides files needed to run the simulations described in the manuscript entitled "Organic contaminants and atmospheric nitrogen at the graphene\u2013water interface: A simulation study" using the molecular dynamics software NAMD and LAMMPS. The output of the simulations, as well as scripts used to analyze this output, are also included. The files are organized into directories corresponding to the figures of the main text and supplementary information. They include molecular model structure files (NAMD psf), force field parameter files (in CHARMM format), initial atomic coordinates (pdb format), NAMD or LAMMPS configuration files, Colvars configuration files, NAMD log files, and NAMD output including restart files (in binary NAMD format) and some trajectories in dcd format (downsampled). Analysis is controlled by shell scripts (Bash-compatible) that call VMD Tcl scripts. A modified LAMMPS C++ source file is also included.<\/p>"],"Other":["This material is based upon work supported by the 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) and Stampede2 at the Texas Advanced Computing Center through allocation BIO200030, which is supported by National Science Foundation grant number ACI-1548562."]} 

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4. Simulation files for "Interfacial water is separated from a hydrophobic silica surface by a gap of 1.2 nm"

   https://doi.org/10.5281/zenodo.14855068  

   Comer, Jeffrey (February 2025, Zenodo)

   This is the simulation data set for the manuscript: Arvelo DM, Comer J, Schmit J, Garcia R (2024) Interfacial water is separated from a hydrophobic silica surface by a gap of 1.2 nm. ACS Nano 18:18683–18692. https://doi.org/10.1021/acsnano.4c05689 This data set 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. LAMMPS input files for the ReaxFF simulations are also included. 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 LAMMPS data), force field parameter files (in CHARMM format or ReaxFF format), initial atomic coordinates (pdb format), NAMD or LAMMPS configuration files, Colvars configuration files, NAMD or LAMMPS log files, and output including restart files (in binary NAMD format) and trajectories in dcd format (downsampled with a stride of 100 to 20 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. Version: 1.0. Figure5AC: Simulation of pentadecane on a 5 chains/nm^2 OTS layer. Figure5B_FigureS7: Calculation of force profile for an SiO2 tip asperity model using adaptive biasing force. Systems: octane with 5 chains/nm^2 OTS, octane with 4 chains/nm^2 OTS, decane with 5 chains/nm^2 OTS, water with 5 chains/nm^2 OTS. FigureS6: Simulations showing the effect of octadecane on the structure of the OTS layer for 3 and 5 chains/nm^2 densities. FigureS8: Calculation of the adsorption free energy of tetracosane (C24) at the OTS–water interface using ABF. FigureS9: Python script for estimating the critical concentration to form an alkane layer at the OTS–water interface using the mean-field Ising model. FigureS10: ReaxFF simulation and modeling to create the silanol-terminated amorphous silica model of an AFM tip asperity. FigureS11: Molecular dynamics simulations showing spontaneous assembly of twelve or twenty-four tetracosane (C24) molecules at the interface between water and the alkyl groups of an OTS-conjugated silica surface. 

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5. Experimentation Framework for Wireless Communication Systems under Jamming Scenarios Dataset

   https://doi.org/10.5281/zenodo.4749668  

   Jacovic, Marko (January 2021, Zenodo)

   {"Abstract":["Data files were used in support of the research paper titled "\u201cExperimentation Framework for Wireless\nCommunication Systems under Jamming Scenarios" which has been submitted to the IET Cyber-Physical Systems: Theory & Applications journal. <\/p>\n\nAuthors: Marko Jacovic, Michael J. Liston, Vasil Pano, Geoffrey Mainland, Kapil R. Dandekar\nContact: krd26@drexel.edu<\/p>\n\n---------------------------------------------------------------------------------------------<\/p>\n\nTop-level directories correspond to the case studies discussed in the paper. Each includes the sub-directories: logs, parsers, rayTracingEmulation, results. <\/p>\n\n--------------------------------<\/p>\n\nlogs:    - data logs collected from devices under test\n    - 'defenseInfrastucture' contains console output from a WARP 802.11 reference design network. Filename structure follows '*x*dB_*y*.txt' in which *x* is the reactive jamming power level and *y* is the jaming duration in samples (100k samples = 1 ms). 'noJammer.txt' does not include the jammer and is a base-line case. 'outMedian.txt' contains the median statistics for log files collected prior to the inclusion of the calculation in the processing script. \n    - 'uavCommunication' contains MGEN logs at each receiver for cases using omni-directional and RALA antennas with a 10 dB constant jammer and without the jammer. Omni-directional folder contains multiple repeated experiments to provide reliable results during each calculation window. RALA directories use s*N* folders in which *N* represents each antenna state. \n    - 'vehicularTechnologies' contains MGEN logs at the car receiver for different scenarios. 'rxNj_5rep.drc' does not consider jammers present, 'rx33J_5rep.drc' introduces the periodic jammer, in 'rx33jSched_5rep.drc' the device under test uses time scheduling around the periodic jammer, in 'rx33JSchedRandom_5rep.drc' the same modified time schedule is used with a random jammer. <\/p>\n\n--------------------------------<\/p>\n\nparsers:    - scripts used to collect or process the log files used in the study\n        - 'defenseInfrastructure' contains the 'xputFiveNodes.py' script which is used to control and log the throughput of a 5-node WARP 802.11 reference design network. Log files are manually inspected to generate results (end of log file provides a summary). \n        - 'uavCommunication' contains a 'readMe.txt' file which describes the parsing of the MGEN logs using TRPR. TRPR must be installed to run the scripts and directory locations must be updated. \n        - 'vehicularTechnologies' contains the 'mgenParser.py' script and supporting 'bfb.json' configuration file which also require TRPR to be installed and directories to be updated. <\/p>\n\n--------------------------------<\/p>\n\nrayTracingEmulation:    - 'wirelessInsiteImages': images of model used in Wireless Insite\n            - 'channelSummary.pdf': summary of channel statistics from ray-tracing study\n            - 'rawScenario': scenario files resulting from code base directly from ray-tracing output based on configuration defined by '*WI.json' file \n            - 'processedScenario': pre-processed scenario file to be used by DYSE channel emulator based on configuration defined by '*DYSE.json' file, applies fixed attenuation measured externally by spectrum analyzer and additional transmit power per node if desired\n            - DYSE scenario file format: time stamp (milli seconds), receiver ID, transmitter ID, main path gain (dB), main path phase (radians), main path delay (micro seconds), Doppler shift (Hz), multipath 1 gain (dB), multipath 1 phase (radians), multipath 1 delay relative to main path delay (micro seconds), multipath 2 gain (dB), multipath 2 phase (radians), multipath 2 delay relative to main path delay (micro seconds)\n            - 'nodeMapping.txt': mapping of Wireless Insite transceivers to DYSE channel emulator physical connections required\n            - 'uavCommunication' directory additionally includes 'antennaPattern' which contains the RALA pattern data for the omni-directional mode ('omni.csv') and directional state ('90.csv')<\/p>\n\n--------------------------------<\/p>\n\nresults:    - contains performance results used in paper based on parsing of aforementioned log files\n <\/p>"]} 

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