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NAMD Standard Output Up: NAMD Tutorial Previous: Parameter Files. NAMD Configuration Files The NAMD configuration file (also called a config file, .conf file, or .namd file) is given to NAMD
NAMD 2.7b3 - Download - Softpedia
NITROGEN MAINTENANCE To keep supervisory nitrogen or air pressure at the correct level in and preaction sprinkler systems Also used for the same purpose in the dry line of a dry pilot actuated deluge valve NAMD 1119660 UL cUL CE 35 140 1.6 60 and up to 99 relative humidity Connection Inch NPT Female 200psi 13.79 bar Max Bulletin 5403713 Requirements NFPA 13 2019 section 8.2.6.6 requires that each dry pipe with an air compressor capable of supplying equal to or greater than 5.5 160 L min at 10 psi 0.7 bar be provided with a listed dedicated air device Questions How does an Air Maintenance Device AMD work The AMD reduces the downstream pressure to the level required provided the valve manufacturer and allows small amounts of air nitrogen to enter system through a 3 32 orifice as needed for small leaks When the system the sudden loss of air nitrogen overcomes the AMD ability to supply through the small orifice and allows the valve to open Where does the AMD get installed The AMD is installed between an air or nitrogen supply which is at a higher than the pressure needed for the system to properly operate and the or preaction sprinkler system E A T U R E S Corrosion resistant all brass 2 dial pressure gauge included Easily adjusted without tools Information Air Device View more information about the Nitrogen Air Maintenance Device including Specs Visit pttr us NAMD Electric Signal Company LLC sales pottersignal com 866 956 1211 www pottersignal com. NAMD Standard Output Up: NAMD Tutorial Previous: Parameter Files. NAMD Configuration Files The NAMD configuration file (also called a config file, .conf file, or .namd file) is given to NAMD Download NAMD Download VMD NamdWiki RecentChanges Preferences. Search Wiki NAMD Wiki: NamdWiki Download NAMD Download VMD NamdWiki RecentChanges Preferences. Search Wiki NAMD Wiki: NamdPerformanceTuning Download NAMD Download VMD NamdWiki RecentChanges Preferences. Search Wiki NAMD Wiki: NamdTroubleshooting What kind of malware is Kitz?Kitz is ransomware that uses encryption to lock files on the target's computer. Our team came across Kitz while reviewing recently submitted malware samples on VirusTotal. This particular ransomware is a member of the Djvu ransomware family and may be distributed in conjunction with other types of malware, such as RedLine or Vidar.When Kitz infects a computer, it appends the ".kitz" extension to the filename of each encrypted file and drops a ransom note (a file namd "_readme.txt"). For example, it renames "1.jpg" to "1.jpg.kitz", "2.png" to "2.png.kitz", and so forth.Screenshot of files encrypted by Kitz ransomware:Kitz ransom note overviewAccording to the note, a particular decryption tool and a unique key are required to decrypt the files, which the attackers offer to sell for either $980 or $490, depending on when the victim contacts them - either within or after 72 hours.The ransom note includes two email addresses ([email protected] and [email protected]) to communicate with the attackers. The note also states that victims can test the decryption process by sending a single encrypted file before committing to purchasing the decryption tools.More about ransomwareTypically, victims cannot decrypt files without tools purchased from cybercriminals. However, there are alternative solutions available to victims instead of paying the ransom to retrieve their files. For instance, victims search for functional third-party decryption tools online or use data backups (if they exist and were created before the attack).It is strongly recommended not to give in to ransom demands, as this not only encourages attackers to continue their illegal activities but also offers no guarantee of receiving the decryption tools or retrieving the encrypted files.Ransomware is harmful malware that can cause further infections and encryptions. Thus, victims should eliminate ransomware from infected systems as soon as they can.Ransomware in generalIn ransomware attacks, data encryption is a typical occurrence, with the ransomware variant adding its extension to the filenames of all encrypted files. Along with the encrypted files, ransom notes, typically pop-up windows or text files, are often included in attacks. Examples of different ransomware variants are Rorschach, Proton, and BlackByteNT.How did ransomware infect my computer?Threat actors disseminate Djvu ransomware via malicious email attachments or links, web pages offering pirated or cracked software, and sites offering users to download videos from YouTube.Additionally, users often inadvertently infect their computers with ransomware by downloading files from untrustworthy sources, including Peer-to-Peer networks, free file hosting sites, third-partyComments
NITROGEN MAINTENANCE To keep supervisory nitrogen or air pressure at the correct level in and preaction sprinkler systems Also used for the same purpose in the dry line of a dry pilot actuated deluge valve NAMD 1119660 UL cUL CE 35 140 1.6 60 and up to 99 relative humidity Connection Inch NPT Female 200psi 13.79 bar Max Bulletin 5403713 Requirements NFPA 13 2019 section 8.2.6.6 requires that each dry pipe with an air compressor capable of supplying equal to or greater than 5.5 160 L min at 10 psi 0.7 bar be provided with a listed dedicated air device Questions How does an Air Maintenance Device AMD work The AMD reduces the downstream pressure to the level required provided the valve manufacturer and allows small amounts of air nitrogen to enter system through a 3 32 orifice as needed for small leaks When the system the sudden loss of air nitrogen overcomes the AMD ability to supply through the small orifice and allows the valve to open Where does the AMD get installed The AMD is installed between an air or nitrogen supply which is at a higher than the pressure needed for the system to properly operate and the or preaction sprinkler system E A T U R E S Corrosion resistant all brass 2 dial pressure gauge included Easily adjusted without tools Information Air Device View more information about the Nitrogen Air Maintenance Device including Specs Visit pttr us NAMD Electric Signal Company LLC sales pottersignal com 866 956 1211 www pottersignal com
2025-04-07What kind of malware is Kitz?Kitz is ransomware that uses encryption to lock files on the target's computer. Our team came across Kitz while reviewing recently submitted malware samples on VirusTotal. This particular ransomware is a member of the Djvu ransomware family and may be distributed in conjunction with other types of malware, such as RedLine or Vidar.When Kitz infects a computer, it appends the ".kitz" extension to the filename of each encrypted file and drops a ransom note (a file namd "_readme.txt"). For example, it renames "1.jpg" to "1.jpg.kitz", "2.png" to "2.png.kitz", and so forth.Screenshot of files encrypted by Kitz ransomware:Kitz ransom note overviewAccording to the note, a particular decryption tool and a unique key are required to decrypt the files, which the attackers offer to sell for either $980 or $490, depending on when the victim contacts them - either within or after 72 hours.The ransom note includes two email addresses ([email protected] and [email protected]) to communicate with the attackers. The note also states that victims can test the decryption process by sending a single encrypted file before committing to purchasing the decryption tools.More about ransomwareTypically, victims cannot decrypt files without tools purchased from cybercriminals. However, there are alternative solutions available to victims instead of paying the ransom to retrieve their files. For instance, victims search for functional third-party decryption tools online or use data backups (if they exist and were created before the attack).It is strongly recommended not to give in to ransom demands, as this not only encourages attackers to continue their illegal activities but also offers no guarantee of receiving the decryption tools or retrieving the encrypted files.Ransomware is harmful malware that can cause further infections and encryptions. Thus, victims should eliminate ransomware from infected systems as soon as they can.Ransomware in generalIn ransomware attacks, data encryption is a typical occurrence, with the ransomware variant adding its extension to the filenames of all encrypted files. Along with the encrypted files, ransom notes, typically pop-up windows or text files, are often included in attacks. Examples of different ransomware variants are Rorschach, Proton, and BlackByteNT.How did ransomware infect my computer?Threat actors disseminate Djvu ransomware via malicious email attachments or links, web pages offering pirated or cracked software, and sites offering users to download videos from YouTube.Additionally, users often inadvertently infect their computers with ransomware by downloading files from untrustworthy sources, including Peer-to-Peer networks, free file hosting sites, third-party
2025-03-26End of a MD are the richest and most complete in terms of non-quantum simulation [2]. However, implementing a MD experiment is not trivial [3].Since its first applied approach to biology in 1977 much has evolved due to increased computational processing as well as improved coding. More than three decades ago, the first MD softwares that were intended for biological problems were launched: Gromacs [4], AMBER [5] and NAMD [6]. Since its first versions, these softwares still remain as the most used and cited. However, they continue with the same common implementation difficulties that plague researchers who are not computer specialists [3].The paradigm of how software is executed has evolved as computing resources have improved. The first digital paradigm was the command line interfaces (CLI) followed by the evolution to the known graphical user interfaces (GUI) [7]. Following the evolutionary cycle, the interface produced by the World Wide Web (or simply WEB) is considered as an evolution of GUIs. These three paradigms currently co-exist depending on developers. Structural Bioinformatics software most commonly uses CLI and GUI paradigms. Some examples of classic software that use CLI are Modeller [8] for similarity modeling, Autodock [9] for molecular docking and Gromacs [4] for molecular dynamics. Examples of software that adopt the GUI type are SwissPDBviewer [10], Pymol [11], VMD [12], USCF Chimera [13], among others. With the emergence of HTML5 (Hypertext Markup Language version 5) [14], CSS (Cascading Style Sheets) [15], Javascript [16] technologies, among others, the development for WEB of many applications for structural bioinformatics could be rewritten to function in this new paradigm. Examples of similarity modeling web servers are: MODWEB [17] which uses Modeller as a back-end and Swissmodel [18]. Examples of web application servers for molecular docking are Haddock [19], Swissdock [20], Cluspro [21] and others.While structural analysis, modeling
2025-03-27Other topologies with more improved loading methods. The group's objective is also to implement its own methodology to calculate partial charges and topologies directly on the software, thus allowing to reduce steps.Availability and requirementsProject name: VisualDynamics. Project home page: Operating system: Linux. Programming language: Python 3.5 or higher, Flask, HTML5. Other requirements: GROMACS 2018 or higher; Grace or Xmgrace. License: FreeBSD. Any restrictions to use by non-academics: None. Availability of data and materials All sources codes are freely available at AbbreviationsMD: Molecular dynamics VD: VisualDynamics CLI: Command line interfaces GUI: Graphical user interfaces WEB: World Wide Web VMD: Visual molecular dynamics ACPYPE: Antechamber python parser interface ReferencesAdcock SA, McCammon JA. Molecular dynamics: survey of methods for simulating the activity of proteins. Chem Rev. 2006;106(5):1589–615.Article CAS PubMed PubMed Central Google Scholar Stillinger FH, Rahman A. Improved simulation of liquid water by molecular dynamics. J Chem Phys. 1974;60(4):1545–57.Article CAS Google Scholar Zinovjev K, van der Kamp MW. Enlighten2: molecular dynamics simulations of protein-ligand systems made accessible. Bioinform. 2020;36(20):5104–6.Article CAS Google Scholar Berendsen HJC, van der Spoel D, van Drunen R. GROMACS: a message-passing parallel molecular dynamics implementation. Comput Phys Commun. 1995;91(1–3):43–56.Article CAS Google Scholar Pearlman DA, Caseb DA, Caldwell JW, Ross WS, Cheatham TE III, DeBolt S, et al. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput Phys Commun. 1995;91(1–3):1–41.Article CAS Google Scholar Nelson MT, Humphrey W, Gursoy A, Dalke A, Kalé LV, Skeel RD, Schulten K. NAMD: a parallel, object-oriented molecular dynamics program. Int J Supercomput Appl High Perform Comput. 1996;10(4):251–68. Google Scholar Wigdor D, Wixon D. Brave NUI world: designing natural user interfaces for touch and gesture. Elsevier; 2011.Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen
2025-04-13(ex: amino acid residues in the binding site may be involved in binding).Ligand selection and preparationStructural information of a ligand molecule or atom or ion can be obtained similarly from any structural database, including PubChem, DrugBank, and PDB etc. or drawn using any chemical molecule drawing tool, like ChemDraw, Avogadro, ChemIDplus, ACD/ChemSketch freeware, BIOVIA Draw, ChemSpider, and PubChem Sketcher, etc. [22, 23, 39,40,41,42,43,44]. They should be treated as flexible bodies as well except for ring conformations. The number of rotatable bonds is calculated. The more the number of rotatable bonds, the more difficult and time-consuming the docking process will be due to the increase in search space. The ligand geometry should be optimized to have a stable conformation by any structure optimization tool, such as Avogadro, UCSF Chimera’s Dock Prep, NAMD tool and the atomic partial charges are then assigned to it by partial charges addition tool, such as UCSC Chimera (Table 2).Table 2 List of software programs/web servers used for different steps in docking processFull size tableDockingThe ligand can be docked into the binding pocket of the receptor either using the known location of the active site (active-site docking) or searching for it (blind docking). If the structure of a holoprotein (protein bound with ligand) gets available then the binding site information can be useful for active-site docking. Otherwise, binding site prediction tools, namely LigASite [45] can be useful to predict the binding pocket information. In the molecular docking process, the search space to fit the ligand is explored considering the flexibility of both receptor and ligand.Different approaches used to predict the binding site depend on (1) templates, (2) energy functions, (3) geometric considerations, and (4) machine learning [46]. The template-based approach predicts the binding site of a given protein using well-studied proteins having similar structures with known binding pocket information. The energy-based approach guesses the binding pocket information by using energetically favorable regions of the protein to bind the ligand in it. The geometry-based approach uses the geometry of the protein to find binding pocket of it. Machine learning approaches learn from existing vast amount of high-resolution protein
2025-04-03The Calculix finite-element analysis program to model a jet engine turbine's internal temperature. The Catia workload uses the catia-05 viewset from SPECviewperf 13 to replay traces generated by Dassault Systemes' CATIA V6 R2012 3D CAD application. The Creo workload uses the creo-02 viewset from SPECviewperf 13 to replay traces generated by PTC's Creo, a 3D CAD application. The NX workload uses the snx-03 viewset from SPECviewperf 13 to replay traces generated by the Siemens PLM NX 8.0 CAD/CAM/CAE application. The Solidworks workload uses the sw-04 viewset from SPECviewperf 13 to replay traces generated by Dassault Systemes' SolidWorks 2013 SP1 CAD/CAE application. The Showcase workload uses the showcase-02 viewset from SPECviewperf 13 to replay traces from Autodesk's Showcase 2013 3D visualization and presentation applicationLife SciencesThe Life Sciences category comprises of four distinct test sets: The LAMMPS set comprises of five tests simulating different molecular properties using the LAMMPS molecular dynamics simulator. The NAMD set comprises of three tests simulating different molecular interactions. The Rodinia (Life Sciences) set comprises of four tests - the Heartwall medical imaging algorithm, the Lavamd algorithm for calculation of particle potential and relocation in a 3D space due to mutual forces, the Hotspot algorithm to estimate processor temperature with thermal simulations, and the SRAD anisotropic diffusion algorithm for denoising. The Medical workload uses the medical-02 viewset from SPECviewperf 13 to determine system performance for the Tuvok rendering core in the ImageVis3D volume visualization program.Financial ServicesThe Financial Services workload set benchmarks the system for three popular algorithms used in the financial services industry - the Monte Carlo probability simulation for risk assessment and forecast modeling, the Black-Scholes pricing model, and the Binomial Options pricing model.EnergyThe Energy category comprises of workloads simulating various algorithms used in the oil and gas industry: The FFTW workload computes discrete Fourier transforms of large matrices. The Convolution workload computes the convolution of a random 100x100 filter on a 400 megapixel image. The SRMP workload processes the Surface-Related Multiples Prediction algorithm used in seismic data processing. The Kirchhoff Migration workload processes an algorithm to calculate the back propogation of a seismic wavefield. The Poisson workload takes advantage of the OpenMP multi-processing framework to solve the Poisson's equation. The Energy workload uses the energy-02 viewset from SPECviewperf 13 to determine system performance for the open-source OPendTec seismic visualization application.General OperationsIn the General Options category, the focus is on workloads from widely used applications in the workstation market: The 7zip workload represents compression and decompression operations using the open-source 7zip file archiver program. The Python workload benchmarks math operations using the numpy and scipy libraries along with other Python features. The Octave workload performs math operations using the Octave programming language used in scientific computing. The
2025-04-07