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id stringlengths 40 40	title stringlengths 15 120	text stringlengths 41 3.14k	source stringclasses 2 values
1f3fc93e14206b2b0c6977b308534a97ae66fa1f	molecular dynamics (md) is a computer simulation method	molecular dynamics (md) is a computer simulation method for analyzing the physical movements of atoms and molecules. the atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. in the most common version, the trajectories of atoms and molecules are...	wikipedia
c8f3cfcd64e2d445b1b2cb2447c3091789ac2f7d	a lot of important applications of smd are	a lot of important applications of smd are in the field of drug discovery and biomolecular sciences. for e.g. smd was used to investigate the stability of alzheimer's protofibrils, to study the protein ligand interaction in cyclin-dependent kinase 5 and even to show the effect of electric field on thrombin (protein) an...	wikipedia
919ce260d67393662e6f09772b3a8216d1d6b020	there are two typical protocols of smd: one	there are two typical protocols of smd: one in which pulling velocity is held constant, and one in which applied force is constant. typically, part of the studied system (e.g., an atom in a protein) is restrained by a harmonic potential. forces are then applied to specific atoms at either a constant velocity or a const...	wikipedia
2af49b356d5598fc3423e2ac9b58164cfbeae3a0	steered molecular dynamics (smd) simulations, or force probe	steered molecular dynamics (smd) simulations, or force probe simulations, apply forces to a protein in order to manipulate its structure by pulling it along desired degrees of freedom. these experiments can be used to reveal structural changes in a protein at the atomic level. smd is often used to simulate events such ...	wikipedia
6bf51b6e520cb2e0c3f10b731393631c8ac06b24	a long range interaction is an interaction in	a long range interaction is an interaction in which the spatial interaction falls off no faster than r − d {\displaystyle r^{-d}} where d {\displaystyle d} is the dimensionality of the system. examples include charge-charge interactions between ions and dipole-dipole interactions between molecules. modelling these forc...	wikipedia
180c22b67a307a07fe6a0a5b79d0c8280ea505cb	without incorporating the effects of solvent simulations of	without incorporating the effects of solvent simulations of macromolecules (such as proteins) may yield unrealistic behavior and even small molecules may adopt more compact conformations due to favourable van der waals forces and electrostatic interactions which would be dampened in the presence of a solvent.	wikipedia
91e1f7ac5ba916f145f690690213ffbbdf7b6576	in many simulations of a solute-solvent system the	in many simulations of a solute-solvent system the main focus is on the behavior of the solute with little interest of the solvent behavior particularly in those solvent molecules residing in regions far from the solute molecule. solvents may influence the dynamic behavior of solutes via random collisions and by imposi...	wikipedia
4141f0eebd2f51a1f207afafb570688993040f65	the polar hydrogens are usually retained in the	the polar hydrogens are usually retained in the model, because proper treatment of hydrogen bonds requires a reasonably accurate description of the directionality and the electrostatic interactions between the donor and acceptor groups. a hydroxyl group, for example, can be both a hydrogen bond donor, and a hydrogen bo...	wikipedia
f98a203f7c2ed5425b3c0d95d59e7a9ae628d463	the simplest form of coarse-graining is the united	the simplest form of coarse-graining is the united atom (sometimes called extended atom) and was used in most early md simulations of proteins, lipids, and nucleic acids. for example, instead of treating all four atoms of a ch methyl group explicitly (or all three atoms of ch methylene group), one represents the whole ...	wikipedia
03710b9753567a77d45a2109f519751f3b7ec933	the parameterization of these very coarse-grained models must	the parameterization of these very coarse-grained models must be done empirically, by matching the behavior of the model to appropriate experimental data or all-atom simulations. ideally, these parameters should account for both enthalpic and entropic contributions to free energy in an implicit way. when coarse-grainin...	wikipedia
05b0c3de1dd8f696e2102703c7c9e9eabfc11ec6	examples for coarse graining (cg) methods are discontinuous	examples for coarse graining (cg) methods are discontinuous molecular dynamics (cg-dmd) and go-models. coarse-graining is done sometimes taking larger pseudo-atoms. such united atom approximations have been used in md simulations of biological membranes. implementation of such approach on systems where electrical prope...	wikipedia
942818484772c181ee314650a6113952049ea6ee	at the other end of the detail scale	at the other end of the detail scale are coarse-grained and lattice models. instead of explicitly representing every atom of the system, one uses "pseudo-atoms" to represent groups of atoms. md simulations on very large systems may require such large computer resources that they cannot easily be studied by traditional ...	wikipedia
cb8582e42e2781be369842580808abe4909612a7	in more sophisticated implementations, qm/mm methods exist to	in more sophisticated implementations, qm/mm methods exist to treat both light nuclei susceptible to quantum effects (such as hydrogens) and electronic states. this allows generating hydrogen wave-functions (similar to electronic wave-functions). this methodology has been useful in investigating phenomena such as hydro...	wikipedia
8dd81e4de74ff9c0ba30668bfa3159affafc641e	the most important advantage of hybrid qm/mm method	the most important advantage of hybrid qm/mm method is the speed. the cost of doing classical molecular dynamics (mm) in the most straightforward case scales o(n), where n is the number of atoms in the system. this is mainly due to electrostatic interactions term (every particle interacts with every other particle). ho...	wikipedia
a48942100a461f3e51291a97e33293a058eba859	qm (quantum-mechanical) methods are very powerful. however, they	qm (quantum-mechanical) methods are very powerful. however, they are computationally expensive, while the mm (classical or molecular mechanics) methods are fast but suffer from several limits (require extensive parameterization; energy estimates obtained are not very accurate; cannot be used to simulate reactions where...	wikipedia
60989a6733e17753eacae5bf018afad929326746	ab initio quantum mechanical and chemical methods may	ab initio quantum mechanical and chemical methods may be used to calculate the potential energy of a system on the fly, as needed for conformations in a trajectory. this calculation is usually made in the close neighborhood of the reaction coordinate. although various approximations may be used, these are based on theo...	wikipedia
19be2a85619b202d46c76433cd427fd7ce22ac80	in classical molecular dynamics, one potential energy surface	in classical molecular dynamics, one potential energy surface (usually the ground state) is represented in the force field. this is a consequence of the born–oppenheimer approximation. in excited states, chemical reactions or when a more accurate representation is needed, electronic behavior can be obtained from first ...	wikipedia
65875f53dfe6110b48a4217b6bf7bd3b72dfe5fa	for many years, polarizable md simulations have been	for many years, polarizable md simulations have been touted as the next generation. for homogenous liquids such as water, increased accuracy has been achieved through the inclusion of polarizability. some promising results have also been achieved for proteins. however, it is still uncertain how to best approximate pola...	wikipedia
4d1e74e29487d4197e123c4eb854179cb6151e12	most classical force fields implicitly include the effect	most classical force fields implicitly include the effect of polarizability, e.g., by scaling up the partial charges obtained from quantum chemical calculations. these partial charges are stationary with respect to the mass of the atom. but molecular dynamics simulations can explicitly model polarizability with the int...	wikipedia
5ac1f784ce7c8911b5c429d2e5e4ef69760f6c6f	semi-empirical potentials make use of the matrix representation	semi-empirical potentials make use of the matrix representation from quantum mechanics. however, the values of the matrix elements are found through empirical formulae that estimate the degree of overlap of specific atomic orbitals. the matrix is then diagonalized to determine the occupancy of the different atomic orbi...	wikipedia
533151d7d23cf2a46fd52b74604be874699f0746	in many-body potentials, the potential energy includes the	in many-body potentials, the potential energy includes the effects of three or more particles interacting with each other. in simulations with pairwise potentials, global interactions in the system also exist, but they occur only through pairwise terms. in many-body potentials, the potential energy cannot be found by a...	wikipedia
d83ba0b5e5a40810c76a2d2df96c91c6214a0b9a	another example is the born (ionic) model of	another example is the born (ionic) model of the ionic lattice. the first term in the next equation is coulomb's law for a pair of ions, the second term is the short-range repulsion explained by pauli's exclusion principle and the final term is the dispersion interaction term. usually, a simulation only includes the di...	wikipedia
2ad96b1903932f3c3ec0653084317469b63bdd38	the potential functions representing the non-bonded energy are	the potential functions representing the non-bonded energy are formulated as a sum over interactions between the particles of the system. the simplest choice, employed in many popular force fields, is the "pair potential", in which the total potential energy can be calculated from the sum of energy contributions betwee...	wikipedia
4a9c010f783ad3332b45554d9b07582968ca857c	chemistry force fields commonly employ preset bonding arrangements	chemistry force fields commonly employ preset bonding arrangements (an exception being ab initio dynamics), and thus are unable to model the process of chemical bond breaking and reactions explicitly. on the other hand, many of the potentials used in physics, such as those based on the bond order formalism can describe...	wikipedia
4c2f8cc258c6e199729837f59776eca49fdec060	because of the non-local nature of non-bonded interactions,	because of the non-local nature of non-bonded interactions, they involve at least weak interactions between all particles in the system. its calculation is normally the bottleneck in the speed of md simulations. to lower the computational cost, force fields employ numerical approximations such as shifted cutoff radii, ...	wikipedia
4233f1421f4b4939679fb6fac0c16357a8c5162b	most force fields in chemistry are empirical and	most force fields in chemistry are empirical and consist of a summation of bonded forces associated with chemical bonds, bond angles, and bond dihedrals, and non-bonded forces associated with van der waals forces and electrostatic charge. empirical potentials represent quantum-mechanical effects in a limited way throug...	wikipedia
909fb59d7b225a2de2c6b2c9086b862ac555381b	when finer levels of detail are needed, potentials	when finer levels of detail are needed, potentials based on quantum mechanics are used; some methods attempt to create hybrid classical/quantum potentials where the bulk of the system is treated classically but a small region is treated as a quantum system, usually undergoing a chemical transformation.	wikipedia
20b3b9cb136d2558cfef76b1242f2d6a46109a8b	the reduction from a fully quantum description to	the reduction from a fully quantum description to a classical potential entails two main approximations. the first one is the born–oppenheimer approximation, which states that the dynamics of electrons are so fast that they can be considered to react instantaneously to the motion of their nuclei. as a consequence, they...	wikipedia
533852ab76125f85dbba981bdcdb421e3ae62d93	a molecular dynamics simulation requires the definition of	a molecular dynamics simulation requires the definition of a potential function, or a description of the terms by which the particles in the simulation will interact. in chemistry and biology this is usually referred to as a force field and in materials physics as an interatomic potential. potentials may be defined at ...	wikipedia
3e1fa6b236c718e5d27dea5429a665986a3c2593	the replica exchange method is a generalized ensemble.	the replica exchange method is a generalized ensemble. it was originally created to deal with the slow dynamics of disordered spin systems. it is also called parallel tempering. the replica exchange md (remd) formulation tries to overcome the multiple-minima problem by exchanging the temperature of non-interacting repl...	wikipedia
d86d741d9713b814020fccc80165fcf2eef568dd	in the isothermal–isobaric ensemble, amount of substance (n),	in the isothermal–isobaric ensemble, amount of substance (n), pressure (p) and temperature (t) are conserved. in addition to a thermostat, a barostat is needed. it corresponds most closely to laboratory conditions with a flask open to ambient temperature and pressure.	wikipedia
5df7eed934d709aa3b959ae409230b3c15bedc7a	a variety of thermostat algorithms are available to	a variety of thermostat algorithms are available to add and remove energy from the boundaries of an md simulation in a more or less realistic way, approximating the canonical ensemble. popular methods to control temperature include velocity rescaling, the nosé–hoover thermostat, nosé–hoover chains, the berendsen thermo...	wikipedia
b1e9222b198a5c5487529388da47970dfdfa77cf	in the canonical ensemble, amount of substance (n),	in the canonical ensemble, amount of substance (n), volume (v) and temperature (t) are conserved. it is also sometimes called constant temperature molecular dynamics (ctmd). in nvt, the energy of endothermic and exothermic processes is exchanged with a thermostat.	wikipedia
da1e412ac90ce5026ef6dc7e1a41a6c95e4e3968	a temperature-related phenomenon arises due to the small	a temperature-related phenomenon arises due to the small number of atoms that are used in md simulations. for example, consider simulating the growth of a copper film starting with a substrate containing 500 atoms and a deposition energy of 100 ev. in the real world, the 100 ev from the deposited atom would rapidly be ...	wikipedia
f65333eccf063283113a5eb9cb70c85c45e12df6	one frequent source of confusion is the meaning	one frequent source of confusion is the meaning of temperature in md. commonly we have experience with macroscopic temperatures, which involve a huge number of particles, but temperature is a statistical quantity. if there is a large enough number of atoms, statistical temperature can be estimated from the instantaneou...	wikipedia
c521c91cf840dd196be1c4bac9f158fd3c3c1d1a	for every time step, each particle's position x	for every time step, each particle's position x {\displaystyle x} and velocity v {\displaystyle v} may be integrated with a symplectic integrator method such as verlet integration. the time evolution of x {\displaystyle x} and v {\displaystyle v} is called a trajectory. given the initial positions (e.g., from theoretic...	wikipedia
c35841654acee84fd6634ac2cd4c4c340e3d10c3	the potential energy function u (x) {\displaystyle u(x)}	the potential energy function u (x) {\displaystyle u(x)} of the system is a function of the particle coordinates x {\displaystyle x}. it is referred to simply as the potential in physics, or the force field in chemistry. the first equation comes from newton's laws of motion; the force f {\displaystyle f} acting on each...	wikipedia
50030e07c8d51205cf9fc26bb269485e64ceaf0c	in the microcanonical ensemble, the system is isolated	in the microcanonical ensemble, the system is isolated from changes in moles (n), volume (v), and energy (e). it corresponds to an adiabatic process with no heat exchange. a microcanonical molecular dynamics trajectory may be seen as an exchange of potential and kinetic energy, with total energy being conserved. for a ...	wikipedia
d7c426866511df050c84980c41d2b94709288c73	in all kinds of molecular dynamics simulations, the	in all kinds of molecular dynamics simulations, the simulation box size must be large enough to avoid boundary condition artifacts. boundary conditions are often treated by choosing fixed values at the edges (which may cause artifacts), or by employing periodic boundary conditions in which one side of the simulation lo...	wikipedia
f1ff45ea7eae9b61df5999fffe78e9f1b38217fa	for simulating molecules in a solvent, a choice	for simulating molecules in a solvent, a choice should be made between an explicit and implicit solvent. explicit solvent particles (such as the tip3p, spc/e and spc-f water models) must be calculated expensively by the force field, while implicit solvents use a mean-field approach. using an explicit solvent is computa...	wikipedia