22 skills found
essex-lab / GrandA Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.
wolberlab / PyrodPyRod - Tracing water molecules in molecular dynamics simulations
forlilab / WaterkitTool to predict water molecules placement and energy in ligand binding sites
gauravsdeshmukh / ChemGCNChemGCN is a graph convolutional network to predict water solubilities of small molecules.
farbod-nobar / GRADEGRADE: A code to determine clathrate hydrate structures. GRADE analyzes atomic positions of water molecules to compute the number of 5(12), 6(2)5(12) and 6(4)5(12) cages and account for their three-dimensional structures. The output of GRADE can be used for visualization of clathrate hydrate evolution in trajectories using software such as VMD (Visual Molecular Dynamics). Four-body order parameter (F4) can also be calculated for trajectories.
Xundrug / MolTautMolTaut, a tool for the rapid generation of favorable states of drug-like molecules in water
JecaTosovic / ConservedWaterSearchPython module for identification of conserved water molecules from molecular dynamics trajectories.
accsc / GAsolGenetic algorithm to convert 3D-RISM solvent densities to explicit water molecules in binding pockets
DCM-UPB / SFG Spectra ToolThis program computes the sum-frequency generation (SFG) spectrum for a give MD trajectory of interfacial water molecules. The program can applied to planar, cylindrical and spherical interfaces
ncrump / StatisticalMechanicsMetropolis Monte Carlo particle simulations for statistical mechanics in Python and Cython. Simulates Lennard-Jones particles using a Markov chain approach in the NVT and NPT ensembles. Includes random number generators, random walks, Ising model example, and a bonus Metropolis simulation of water molecules in the SPC/E model with trial translations and unit quaternion rotations.
eshamay / InterfacemdTools for working with data from molecular dynamics simulations. Trajectory analysis, computational spectroscopy, density plots, distribution functions, atoms/molecules/systems - specializing in aqueous (water) systems made using Amber, Gromacs, and CP2K simulation packages.
concorde-speed / ConcordeDate of Concorde In January of the year 1976 after 29 years of the first to penetrate to the speed of sound military aircraft jet - Two Concord took off together at the same time, one from London and one from Paris, the first airline service ultrasound for travelers. The aircraft Almottaghtan has looked towards the west as if they were Tgaraan - even Tsabakan - the sun. Where they arrived as if they did not Taathrca, in terms of time, in a new event launches air transport stage supersonic passenger wealthy people who do not allow them to narrow their time to stay in the air for long periods. How the project began and evolved, and how the outcome of the remaining Concorde lounges to museums ... This is what Santapah in the following lines: The emergence of the Concorde The deal "supersonic" between England and France was signed in 1962, for the design and construction of the first civilian supersonic plane manufactured by Airbus for them. After long years of arduous efforts and research strenuous, in addition to more than 5,000 hours in the air tunnels, proved to be a form of equity Almstrq with the body long cylinder for aircraft relatively large passengers, it is the best form executable command and control speeds ultrasound. The first two aircraft of this type making and Tjeribhma in 1969, and since then about 20 aircraft of this model, called the "Concord" was produced (the only civilian aircraft that exceed the speed of sound speed), and who serve in the British Airways and Air France in income 1976, the rate of seven aircraft of the British lines and five lines in French. The first fly line is the London - Singapore via Bahrain. In 1976 received Bahrain Airport very important event, which is to start regular flights between Bahrain and London, the fastest of the British Airways sound Concorde, the airport first and the only one who was receiving this type of aircraft in the Middle East, given that the Concorde need to Airports women with special specifications, so they need to take-off and landing runways longer than the regular airports runways, and the noise from the power of their engines leads to smash windows of buildings ordinary airports, and the speed has a crush Madarjha. What Concorde is distinct from other aircraft?Characterized by Concorde slim form in the form of a triangle (delta). And fly faster and higher than other aircraft altitudes, using the "upward vortex" method to accomplish extraordinary mission. For example, while the "Boeing 747" aircraft speed, better known as "jumbo" around 900 km / h (about 84.0 Mach) at an altitude of 35 thousand feet, the Concorde fly quickly 2172 km / h (Mach 2) at an altitude of 60 thousand Foot. It is known that Almaj is the real rate of speed compared to the speed of sound, and is equivalent to an average of 1225 kilometers per hour, so that the speed of sound changes with temperature change, which moves rapidly 1190 km / h at sea level, but it drops to 1060 km / h at an altitude of 36,000 feet above the ground, where the air temperature drops. Because the Place de la Concorde to fly faster than the speed of sound, they differ from the rest of the aircraft on several characteristics. First, in terms of the flow of the fuselage, where you need to own dynamic shape to face severe air resistance at these high speeds, and it is achieved by taking the body form of a high pin tapered, triangular wings tilted back, my head and a tail, and an introduction brushes can be moved to the bottom of takeoffs and landings to be able to see the pilot of the corridor, to the top during flight to improve the flow of the fuselage. Amounting to 83 feet and 8 inches tall plane wings in the company "Oarossbesiak" has produced and supplied surfaces work together Kdvh depth, also works differentially Kjnahat. There is no tip installed inside the concavity of the wing, but no spire parties descend and spin at the same time. The second difference is related engines, where the Concorde's engines proved directly in the wings to avoid the use of any parts of the conductive would crash at high speeds, and the engine fitted with a special friendly hotel to exploit the resulting exhaust for initial combustion cycle combustion again mixing with more new fuel to increase efficient engines and power, where this process provides the engine in the final stage of heating fuel for the production of the required additional power for takeoff and the transition from one phase to the heating of supersonic flight, allowing aircraft takeoff speed of 360 km / h. The useful load carried by the Concorde's less than a third of what was done other than in the weight of the jets under the sound, so it was no reduction in the efficiency of the engine, it is actually the difference between profit and loss. Every Concorde has supplied four-engine aircraft, "Snecma Olympus DS 593," the momentum of 17259 kg. The company "Rolls Royce" design engines, which provided all Dagtin separate engine in order to fuel economy. Each engine and also provided additional Aq. Engine reverse payment system is also equipped. On the other hand, the Concorde is distinct from other aircraft fuel tanks and the presence of more and larger, with four engines burn a tremendous amount of kerosene has more than 25 thousand liters per flight hour. However, the fuel tanks lead a purpose whatever else, which is to maintain the equilibrium plane, where the center to raise the plane travels at high speeds for its center of gravity and then you move amounts of fuel between private additional tanks at the front of the plane and the rear to offset that effect, and returned those quantities at low speed in preparation for landing to bring the situation back to its origin. For example, a flight plan requires the distance between Paris and the French coast on the Atlantic equator at less than the speed of sound speed is determined to 0.93 Mach, to be at the height of about 9000 meters, after which the plane begins to jump quickly to reach the speed of take-off and altitude wanted, it performs speed between the two situations difference to a change in the dynamics of the plane to move from the airline less than the sound quickly to other higher speed of sound, and to overcome this situation, the transfer of fuel in an aircraft using a payment of reservoirs located in the introduction to the reservoirs in the system rear. During the transitional situation between the two modes of ex (between Mach 1 and Mach 1.6) increases air resistance sharply, and at this moment is to break the sound barrier. Once access to 1.7 Mach the captain to stop the internal combustion process, after more than a very plane speed of up to Mach 2, or 2200 km / h, more than twice the speed of sound, which represent the target aircraft speed, while the estimated target of 16000 and 18000 meters altitude. But when approaching landing, the fuel will move to the front of the plane, and the concomitant rise in the plane's nose, to land the plane in a scene it looks like a bird landing on the surface of the water. Finally remains the difference in the fuselage coating, where the Concorde is exposed at high speeds to a very large rise in body temperature as a result of increased friction of air molecules, so they coated special material properties and reflective stronger than those in the other aircraft, capable of dispersing such high temperatures . The fuselage itself is made from a special metal is characterized by a greater capacity to withstand the heat and stress resistance resulting from inflation fuselage resulting in turn from high temperature. The speed of the plane have been identified in the horizontal flight Mach 2.2, which is just before the thermal barrier (which is the speed at which if exceeded temperature increases dramatically), but it has identified the chronological age of the structure of 60,000 flight hours. And making the structure of the aluminum-alloy steel by thermal changes from -35 degrees to +120 degrees, as the flight above the speed limit of the plane requires that the structure is made with a mixture of steel and titanium, which means more weight. Fly the Concorde at the highest altitudes of 50,000 feet, where the air is equal to a tenth of what Tsawiyeh at sea density, and the temperature at that very low altitude, and despite all this work ultrasonic motors with high efficiency. According to reports of the pilots can handle the plane easily. The acceleration of the aircraft and transit speeds TransitionAnd what is characterized travel Balkounkord from other aircraft? Accommodate the Concorde for a hundred passengers and crew consists of a pilot and a flight engineer and his assistant in addition to the six hosts. When quitting, the passenger feels strongly pay back as a result of the launch aircraft from sleep to the speed of 362 km / h in just 30 seconds, which is called the Earth's gravitational force, and quickly reach the maximum height of the plane and penetrate the speed of the sound barrier. In all the flight times travelers can know the speed, through a private display panel installed in front of them, and are entitled to see the curve of the globe and Northern Lights because of the high altitude, which is flying the plane. Travelers can also watch the first layer colors of the atmosphere, where the height of the plane boundary between the first two Tbaktah. It takes Atlantic crossing Balkounkord three and a half hours only, while the that time about nine hours in the other underneath the aircraft sounds. And up the Concorde passengers who starts his journey from London at ten thirty in the morning to New York at nine thirty in the morning, before the date of its launch radios. This of course does not mean a retreat in time, but due to time differences and the short flight time! Over the last quarter-century, Concorde was the five weekly flights between Paris and New York in a record speed of less than 4 hours, at which time it cut the best of conventional aircraft, the same distance in 8 hours. He was landing at Kennedy Airport (according to US time) at eight in the morning, and exiting back to France at the eleventh hour before noon, where businessmen French used to negotiate with the Americans their customers at the airport Salons, without having to go to the business and financial district in Manhattan, and then return to Paris the same day. And to what the fate of the Concorde? I tried both the US and Soviet governments (former) develop similar Balkounkord aircraft, but those attempts ended in retreat, either because the magnitude of the required expenditures on the American side, or the occurrence of accidents due to human error on the Soviet side. Some of these Soviet aircraft had stayed (model "T U-144"), as amended to date, but used in air mail services, also placed some of them in museums, while one of them devoted to project Russian joint US. And remained the Concorde, solo travel of passengers faster than the speed of sound even temporarily suspended service to make adjustments after the accident led to an explosion killed one of them and all of them were. In addition, the high run that made the ticket price between Paris, London and New York round-trip $ 10,000, which led to limited use of the rich and famous costs, as well as what caused the noise and pollution, suffered Concorde most suffered from weak passenger demand for flights, in Following the incident, which came under the air France one in Paris in July 2000 to a near Charles de Gaulle airport hotels, which led to the deaths of 109 people on board and four people on the ground. Consequently After some major attended by experts and investigators, scientists, lawyers, artists, religious leaders and industrialists from different generations, between believers technology and Muslims in terms of authority to the modern age and among those who believe that it is necessary to rein in scientific progress and the development of ethical and legal controls him, took the final decision to stop flights Place de la Concorde. In July of 2003, tens of thousands of lovers of the Concorde gathered along the road to Heathrow Airport in the fog of London, the capital, in a bid farewell final before this model withdraw aircraft from service, after it made its first commercial flight in 1976. This has three Concorde planes reviewing the air before landing at Heathrow Airport in a reference to the termination of commercial flights known aircraft at supersonic speed. And charged the British Airways Concorde plane carrying 100 special guest at the final flight, which launched from Kennedy Airport in New York towards London, penetrated the sound barrier for the last time. Upon entering British airspace acceded Two Concord British Airways, one coming from the city of Edinburgh in Scotland, and the other from the Bay of Biscay west of France. Lovers plane Odalla in July of 2003 in Paris, as well as a pool, in the last trip out between Paris and New York, after a 27-year-old was cut where the distance between the two cities in a matter of three hours and a half. Where he lined up more than 250 workers from the maintenance workers bodyguards honor of the plane at Charles de Gaulle airport, with thousands of French gathered on the edge of the airport to see the plane taking off, holding a banner reading "We love you, Concord." The French lines: that the plane Concorde belong to the humanitarian aviation heritage and must therefore provide an opportunity for more people to see it, and added that it would apply to all of the fleet of Air France Concorde aircraft, which will be displayed every aircraft in museums in France, Germany and the United States, such as the Museum aviation and aerospace in the suburb of "Le Bourget" Paris, the Museum of Aviation near the Scottish capital "Edinburgh". Parts of the plane crashed as sold at Christie's for souvenirs to those who died to travel out, varied between the nose of the plane and the door of cabin leadership and a seat pilot and antenna radar warning in which the two motors of the engines and parts of the dashboard to the instructions and cutlery dishwasher ceramic spoons and silver booklet, worth total amounted to 3.29 million euros, went in favor of a charitable institution of the air France is working in the field of care for the poor children. Last auction for the sale of pieces of a British Airways Concorde has also been established. The British and French companies have announced at the beginning of the month of April of the same year 2003, he stopped Concorde flights after the company "Airbus" that produced externa announced: What's next in the field of transport ultrasonic? American company, "Boeing" is currently working on the supersonic jet, is supposed to be placed in service during the coming years, while filling the attention of European rival, "Airbus" accomplish its flagship aircraft, "Airbus A380 (superjumbo) capable of carrying about 800 passengers, which had been achieved in 2007, while scientists tried to Japanese to develop a model of the plane was enable fly twice as fast as the Concorde, but their experience after the plane landed long model briefly after take-off from the site "Woomera" to launch rockets in the desert south of Australia, and it failed within the project included my company, "Mitsubishi heavy Industries" and "Nissan Motor." He held this paradigm of a length of 11 meters on a rocket, Plans for him to be separated from the booster rocket above the ground, and falling faster than twice the speed of sound, but it got out of control since it was launched. It was supposed to reach the aircraft remotely piloted altitude of 20 thousand meters, before Taud.aly ground faster than twice the speed of sound. The goal was to become a plane "NeXT 1" transport aircraft the fastest in the world to succeed Concorde, with the difference that it will be less noise and damaging to the environment and can accommodate up to 300 passengers: Thus crossed another Concorde SST recent trip mounted aboard a ship in the River Thames sailing from London to the Museum of Flight in Edinburgh, after he has made more than eight thousand flight during which 22 thousand and 768 hours and 56 cut-minute flight, the folded thereby separating mythic unique and important commercial aviation history, a supersonic flight, waiting for what the future holds for us of new inventions ?!
unitaryfoundation / AquapointerPackage applying quantum algorithms to find locations of water molecules in a protein cavity
teomotun / LAMMPS Water Methanol SimulationMolecular Dynamics Simulation of Water-Methanol Mixture to determine physical properties like self-diffusion coefficient, density and shear viscosity for a system consisting of 216 molecules of water and 216 molecules of methanol
MDAnalysis / WaterdynamicsAnalysis of water dynamics in molecular dynamics trajectories and water interactions with other molecules.
flawnson / NN Solubility PredictorA neural network model that predicts the solubility of a given molecule in room temperature water.
jurevito / Molecule SolubilityMolecule water solubility prediction using DeepChem.
yc-How-python / HydrationShellA tool to analyse the distribution of water molecules in the first solvation shell of certain molecules.
chen3262 / VMD H2ocosineVMD script to label water molecules with different colors according to their orientations.
MobleyLab / WaterNESWorkflows to calculate relative free energies using non-equilibrium switching for buried water molecules
