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Assisted Model Building with Energy Refinement ( AMBER ) is the name of a widely-used molecular dynamics software package originally developed by Peter Kollman 's group at the University of California, San Francisco . It has also, subsequently, come to designate a family of force fields for molecular dynamics of biomolecules that can be used both within the AMBER software suite and with many modern computational platforms.

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64-569: The original version of the AMBER software package was written by Paul Weiner as a post-doc in Peter Kollman's laboratory, and was released in 1981. Subsequently, U Chandra Singh expanded AMBER as a post-doc in Kollman's laboratory, adding molecular dynamics and free energy capabilities. The next iteration of AMBER was started around 1987 by a group of developers in (and associated with)

128-442: A ground term ; a term that doesn't contain multiple occurrences of a variable is called a linear term . For example, 2+2 is a ground term and hence also a linear term, x ⋅( n +1) is a linear term, n ⋅( n +1) is a non-linear term. These properties are important in, for example, term rewriting . Given a signature for the function symbols, the set of all terms forms the free term algebra . The set of all ground terms forms

192-991: A backend . Yum extends the functionality of the backend by adding features such as simple configuration for maintaining a network of systems. As another example, the Synaptic Package Manager provides a graphical user interface by using the Advanced Packaging Tool (apt) library, which, in turn, relies on dpkg for core functionality. Alien is a program that converts between different Linux package formats , supporting conversion between Linux Standard Base (LSB) compliant .rpm packages, .deb , Stampede (.slp), Solaris (.pkg) and Slackware ( .tgz , .txz , .tbz, .tlz) packages. In mobile operating systems, Google Play consumes Android application package (APK) package format while Microsoft Store uses APPX and XAP formats. (Both Google Play and Microsoft Store have eponymous package managers.) By

256-468: A cryptographic hash function ), and a list of dependencies necessary for the software to run properly. Upon installation, metadata is stored in a local package database. Package managers typically maintain a database of software dependencies and version information to prevent software mismatches and missing prerequisites. They work closely with software repositories , binary repository managers , and app stores . Package managers are designed to eliminate

320-447: A mathematical object while a formula denotes a mathematical fact. In particular, terms appear as components of a formula. This is analogous to natural language, where a noun phrase refers to an object and a whole sentence refers to a fact. A first-order term is recursively constructed from constant symbols, variables and function symbols . An expression formed by applying a predicate symbol to an appropriate number of terms

384-402: A , b ∈ V N , the term ⟨ ( v → + 0 → ) ∗ a , w → ∗ b ⟩ {\displaystyle \langle ({\vec {v}}+{\vec {0}})*a,{\vec {w}}*b\rangle } is well-sorted, while v → + a {\displaystyle {\vec {v}}+a}

448-425: A binary executable package on the same or remote computer. Later a package manager typically running on some other computer downloads those pre-built binary executable packages over the internet and installs them. However, both kinds of tools have many commonalities: A few tools, such as Maak and A-A-P , are designed to handle both building and deployment, and can be used as either a build automation utility or as

512-558: A challenge colloquially known as " dependency hell ". On Microsoft Windows systems, this is also called " DLL hell " when working with dynamically linked libraries. Modern package managers have mostly solved these problems, by allowing parallel installation of multiple versions of a library (e.g. OPENSTEP 's Framework system), a dependency of any kind (e.g. slots in Gentoo Portage ), and even of packages compiled with different compiler versions (e.g. dynamic libraries built by

576-614: A large extent translatable, as most package managers offer similar functions. The Arch Linux Pacman/Rosetta wiki offers an extensive overview. Package managers like dpkg have existed as early as 1994. Linux distributions oriented to binary packages rely heavily on package management systems as their primary means of managing and maintaining software. Mobile operating systems such as Android (Linux-based), iOS ( Unix-based ), and Windows Phone rely almost exclusively on their respective vendors' app stores and thus use their own dedicated package management systems. A package manager

640-449: A large number of computers. This kind of pre-configured installation is also supported by dpkg. To give users more control over the kinds of software that they are allowing to be installed on their system (and sometimes due to legal or convenience reasons on the distributors' side), software is often downloaded from a number of software repositories . When a user interacts with the package management software to bring about an upgrade, it

704-896: A loose association of mostly academic labs. New versions are released usually in the spring of even numbered years; AMBER 10 was released in April 2008. The software is available under a site license agreement, which includes full source, currently priced at US$ 500 for non-commercial and US$ 20,000 for commercial organizations. 1. Duan, Yong; Wu, Chun; Chowdhury, Shibasish; Lee, Mathew C.; Xiong, Guoming; Zhang, Wei; Yang, Rong; Cieplak, Piotr; et al. (2003). "A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations". Journal of Computational Chemistry . 24 (16): 1999–2012. doi : 10.1002/jcc.10349 . PMID   14531054 . S2CID   283317 . Software package (installation) A package manager or package-management system

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768-421: A mathematical object from the domain of discourse . A constant c denotes a named object from that domain, a variable x ranges over the objects in that domain, and an n -ary function f maps n - tuples of objects to objects. For example, if n ∈ V is a variable symbol, 1 ∈ C is a constant symbol, and add ∈ F 2 is a binary function symbol, then n ∈ T , 1 ∈ T , and (hence) add ( n , 1) ∈ T by

832-468: A package manager or both. App stores can also be considered application-level package managers (without the ability to install all levels of programs ). Unlike traditional package managers, app stores are designed to enable payment for the software itself (instead of for software development), and may only offer monolithic packages with no dependencies or dependency resolution. They are usually extremely limited in their management functionality, due to

896-409: A relation symbol set R n is usually non-empty only for small n . In mathematical logic, more complex formulas are built from atomic formulas using logical connectives and quantifiers . For example, letting R {\displaystyle \mathbb {R} } denote the set of real numbers , ∀ x : x ∈ R {\displaystyle \mathbb {R} } ⇒ ( x +1)⋅( x +1) ≥ 0

960-485: A strong focus on simplification over power or emergence , and common in commercial operating systems and locked-down “smart” devices. Package managers also often have only human-reviewed code. Many app stores, such and Google Play and Apple's App Store, screen apps mostly using automated tools only; malware with defeat devices can pass these tests, by detecting when the software is being automatically tested and delaying malicious activity. There are, however, exceptions;

1024-421: A term t is called a renaming , or a variant , of a term u if the latter resulted from consistently renaming all variables of the former, i.e. if u = tσ for some renaming substitution σ. In that case, u is a renaming of t , too, since a renaming substitution σ has an inverse σ , and t = uσ . Both terms are then also said to be equal modulo renaming . In many contexts, the particular variable names in

1088-411: A term as a tree. For example, several distinct character strings, like " ( n ⋅( n +1))/2 ", " (( n ⋅( n +1)))/2 ", and " n ( n + 1 ) 2 {\displaystyle {\frac {n(n+1)}{2}}} ", denote the same term and correspond to the same tree, viz. the left tree in the above picture. Separating the tree structure of a term from its graphical representation on paper, it

1152-399: A term don't matter, e.g. the commutativity axiom for addition can be stated as x + y = y + x or as a + b = b + a ; in such cases the whole formula may be renamed, while an arbitrary subterm usually may not, e.g. x + y = b + a is not a valid version of the commutativity axiom. The set of variables of a term t is denoted by vars ( t ). A term that doesn't contain any variables is called

1216-648: A term is also called well-sorted ; any other term (i.e. obeying the unsorted rules only) is called ill-sorted . For example, a vector space comes with an associated field of scalar numbers. Let W and N denote the sort of vectors and numbers, respectively, let V W and V N be the set of vector and number variables, respectively, and C W and C N the set of vector and number constants, respectively. Then e.g. 0 → ∈ C W {\displaystyle {\vec {0}}\in C_{W}} and 0 ∈ C N , and

1280-630: Is CheckInstall , and for recipe-based systems such as Gentoo Linux and hybrid systems such as Arch Linux , it is possible to write a recipe first, which then ensures that the package fits into the local package database. Particularly troublesome with software upgrades are upgrades of configuration files. Since package managers, at least on Unix systems, originated as extensions of file archiving utilities , they can usually only either overwrite or retain configuration files, rather than applying rules to them. There are exceptions to this that usually apply to kernel configuration (which, if broken, will render

1344-405: Is a collection of software tools that automates the process of installing, upgrading, configuring, and removing computer programs for a computer in a consistent manner. A package manager deals with packages , distributions of software and data in archive files . Packages contain metadata , such as the software's name, description of its purpose, version number, vendor, checksum (preferably

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1408-455: Is a mathematical formula evaluating to true in the algebra of complex numbers . An atomic formula is called ground if it is built entirely from ground terms; all ground atomic formulas composable from a given set of function and predicate symbols make up the Herbrand base for these symbol sets. When the domain of discourse contains elements of basically different kinds, it is useful to split

1472-406: Is a software tool designed to optimize the download and storage of binary files, artifacts and packages used and produced in the software development process . These package managers aim to standardize the way enterprises treat all package types. They give users the ability to apply security and compliance metrics across all artifact types. Universal package managers have been referred to as being at

1536-472: Is also easy to account for parentheses (being only representation, not structure) and invisible multiplication operators (existing only in structure, not in representation). Two terms are said to be structurally , literally , or syntactically equal if they correspond to the same tree. For example, the left and the right tree in the above picture are structurally un equal terms, although they might be considered " semantically equal " as they always evaluate to

1600-486: Is called an atomic formula , which evaluates to true or false in bivalent logics , given an interpretation . For example, ⁠ ( x + 1 ) ∗ ( x + 1 ) {\displaystyle (x+1)*(x+1)} ⁠ is a term built from the constant 1, the variable x , and the binary function symbols ⁠ + {\displaystyle +} ⁠ and ⁠ ∗ {\displaystyle *} ⁠ ; it

1664-432: Is customary to present the user with the list of actions to be executed (usually the list of packages to be upgraded, and possibly giving the old and new version numbers), and allow the user to either accept the upgrade in bulk, or select individual packages for upgrades. Many package managers can be configured to never upgrade certain packages, or to upgrade them only when critical vulnerabilities or instabilities are found in

1728-516: Is not (since + doesn't accept a term of sort N as 2nd argument). In order to make a ∗ v → {\displaystyle a*{\vec {v}}} a well-sorted term, an additional declaration ⁠ ∗ : N × W → W {\displaystyle *:N\times W\to W} ⁠ is required. Function symbols having several declarations are called overloaded . See many-sorted logic for more information, including extensions of

1792-418: Is often called an "install manager", which can lead to a confusion between package managers and installers . The differences include: Most software configuration management systems treat building software and deploying software as separate, independent steps. A build automation utility typically takes human-readable source code files already on a computer, and automates the process of converting them into

1856-525: Is part of the atomic formula ⁠ ( x + 1 ) ∗ ( x + 1 ) ≥ 0 {\displaystyle (x+1)*(x+1)\geq 0} ⁠ which evaluates to true for each real-numbered value of x . Besides in logic , terms play important roles in universal algebra , and rewriting systems . Given a set V of variable symbols, a set C of constant symbols and sets F n of n -ary function symbols, also called operator symbols, for each natural number n ≥ 1,

1920-463: Is that free and open source software systems permit third-party packages to also be installed and upgraded through the same mechanism, whereas the package managers of Mac OS X and Windows will only upgrade software provided by Apple and Microsoft, respectively (with the exception of some third party drivers in Windows). The ability to continuously upgrade third-party software is typically added by adding

1984-426: Is to allow users to manage the software dependency on data, such as machine learning models for data-driven applications. They are useful to publish, locate, and install data packages. A typical example of a data dependency management frameworks are Hugging Face, KBox, among others. Ian Murdock had commented that package management is "the single biggest advancement Linux has brought to the industry", that it blurs

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2048-476: The initial term algebra . Abbreviating the number of constants as f 0 , and the number of i -ary function symbols as f i , the number θ h of distinct ground terms of a height up to h can be computed by the following recursion formula: Given a set R n of n -ary relation symbols for each natural number n ≥ 1, an (unsorted first-order) atomic formula is obtained by applying an n -ary relation symbol to n terms. As for function symbols,

2112-477: The Glasgow Haskell Compiler , where a stable ABI does not exist), in order to enable other packages to specify which version they were linked or even installed against. System administrators may install and maintain software using tools other than package management software. For example, a local administrator may download unpackaged source code, compile it, and install it. This may cause

2176-453: The URL of the corresponding repository to the package management's configuration file. Beside the system-level application managers, there are some add-on package managers for operating systems with limited capabilities and for programming languages in which developers need the latest libraries . Unlike system-level package managers, application-level package managers focus on a small part of

2240-404: The lim operator is applied to a sequence, i.e. to a mapping from positive integer to e.g. real numbers. As another example, a C function to implement the second example from the table, Σ, would have a function pointer argument (see box below). Lambda terms can be used to denote anonymous functions to be supplied as arguments to lim , Σ, ∫, etc. For example, the function square from

2304-503: The many-sorted framework described here. Mathematical notations as shown in the table do not fit into the scheme of a first-order term as defined above , as they all introduce an own local , or bound , variable that may not appear outside the notation's scope, e.g. t ⋅ ∫ a b sin ⁡ ( k ⋅ t ) d t {\displaystyle t\cdot \int _{a}^{b}\sin(k\cdot t)\;dt} doesn't make sense. In contrast,

2368-465: The npm package database, for instance, relies entirely on post-publication review of its code, while the Debian package database has an extensive human review process before any package goes into the main stable database. The XZ Utils backdoor used years of trust-building to insert a backdoor, which was nonetheless caught while in the testing database. Also known as binary repository manager , it

2432-556: The sequence ( x /1, x /2, x /3, ...). The lim operator takes such a sequence and returns its limit (if defined). The rightmost column of the table indicates how each mathematical notation example can be represented by a lambda term, also converting common infix operators into prefix form. Given a set V of variable symbols, the set of lambda terms is defined recursively as follows: The above motivating examples also used some constants like div , power , etc. which are, however, not admitted in pure lambda calculus. Intuitively,

2496-455: The AMBER software user manual. Each parameter set has a name, and provides parameters for certain types of molecules. The AMBER software suite provides a set of programs to apply the AMBER forcefields to simulations of biomolecules. It is written in the programming languages Fortran 90 and C , with support for most major Unix-like operating systems and compilers . Development is conducted by

2560-477: The C program below can be written anonymously as a lambda term λ i . i . The general sum operator Σ can then be considered as a ternary function symbol taking a lower bound value, an upper bound value and a function to be summed-up. Due to its latter argument, the Σ operator is called a second-order function symbol . As another example, the lambda term λ n . x / n denotes a function that maps 1, 2, 3, ... to x /1, x /2, x /3, ..., respectively, that is, it denotes

2624-422: The Kollman lab, including David Pearlman, David Case, James Caldwell, William Ross, Thomas Cheatham, Stephen DeBolt, David Ferguson, and George Seibel. This team headed development for more than a decade and introduced a variety of improvements, including significant expansion of the free energy capabilities, accommodation for modern parallel and array processing hardware platforms (Cray, Star, etc.), restructuring of

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2688-403: The abstraction λ x . t denotes a unary function that returns t when given x , while the application ( t 1 t 2 ) denotes the result of calling the function t 1 with the input t 2 . For example, the abstraction λ x . x denotes the identity function, while λ x . y denotes the constant function always returning y . The lambda term λ x .( x x ) takes a function x and returns

2752-460: The boundaries between operating system and applications, and that it makes it "easier to push new innovations [...] into the marketplace and [...] evolve the OS". There is also a conference for package manager developers known as PackagingCon. It was established in 2021 with the aim to understand different approaches to package management. Term (logic) In mathematical logic , a term denotes

2816-482: The center of a DevOps toolchain . Each package manager relies on the format and metadata of the packages it can manage. That is, package managers need groups of files to be bundled for the specific package manager along with appropriate metadata, such as dependencies. Often, a core set of utilities manages the basic installation from these packages and multiple package managers use these utilities to provide additional functionality. For example, yum relies on rpm as

2880-584: The code and revision control for greater maintainability, PME Ewald summations, tools for NMR refinement, and many others. Currently, AMBER is maintained by an active collaboration between David Case at Rutgers University , Tom Cheatham at the University of Utah , Adrian Roitberg at University of Florida , Ken Merz at Michigan State University, Carlos Simmerling at Stony Brook University , Ray Luo at UC Irvine , and Junmei Wang at University of Pittsburgh . The term AMBER force field generally refers to

2944-480: The computer unusable after a restart). Problems can be caused if the format of configuration files changes; for instance, if the old configuration file does not explicitly disable new options that should be disabled. Some package managers, such as Debian 's dpkg , allow configuration during installation. In other situations, it is desirable to install packages with the default configuration and then overwrite this configuration, for instance, in headless installations to

3008-402: The equilibrium distance is r i j 0 {\displaystyle r_{ij}^{0}} . The energy is sometimes reformulated in terms of σ {\displaystyle \sigma } , where r i j 0 = 2 1 / 6 ( σ ) {\displaystyle r_{ij}^{0}=2^{1/6}(\sigma )} , as used e.g. in

3072-409: The first, second, and third term building rule, respectively. The latter term is usually written as n +1, using infix notation and the more common operator symbol + for convenience. Originally, logicians defined a term to be a character string adhering to certain building rules. However, since the concept of tree became popular in computer science, it turned out to be more convenient to think of

3136-1486: The functional form used by the family of AMBER force fields. This form includes several parameters; each member of the family of AMBER force fields provides values for these parameters and has its own name. The functional form of the AMBER force field is + ∑ i ∈ torsions ∑ n 1 2 V i n [ 1 + cos ⁡ ( n ω i − γ i ) ] {\displaystyle +\sum _{i\in {\text{torsions}}}\sum _{n}{\frac {1}{2}}V_{i}^{n}[1+\cos(n\omega _{i}-\gamma _{i})]} + ∑ j = 1 N − 1 ∑ i = j + 1 N f i j { ϵ i j [ ( r i j 0 r i j ) 12 − 2 ( r i j 0 r i j ) 6 ] + q i q j 4 π ϵ 0 r i j } {\displaystyle +\sum _{j=1}^{N-1}\sum _{i=j+1}^{N}f_{ij}{\biggl \{}\epsilon _{ij}{\biggl [}\left({\frac {r_{ij}^{0}}{r_{ij}}}\right)^{12}-2\left({\frac {r_{ij}^{0}}{r_{ij}}}\right)^{6}{\biggr ]}+{\frac {q_{i}q_{j}}{4\pi \epsilon _{0}r_{ij}}}{\biggr \}}} Despite

3200-555: The implementation of the softcore potentials. The form of the electrostatic energy used here assumes that the charges due to the protons and electrons in an atom can be represented by a single point charge (or in the case of parameter sets that employ lone pairs, a small number of point charges.) To use the AMBER force field, it is necessary to have values for the parameters of the force field (e.g. force constants, equilibrium bond lengths and angles, charges). A fairly large number of these parameter sets exist, and are described in detail in

3264-644: The nature of free and open source software , packages under similar and compatible licenses are available for use on a number of operating systems. These packages can be combined and distributed using configurable and internally complex packaging systems to handle many permutations of software and manage version-specific dependencies and conflicts. Some packaging systems of free and open source software are also themselves released as free and open source software. One typical difference between package management in proprietary operating systems, such as Mac OS X and Windows, and those in free and open source software, such as Linux,

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3328-454: The need for manual installs and updates. This can be particularly useful for large enterprises whose operating systems typically consist of hundreds or even tens of thousands of distinct software packages. An early package manager was SMIT (and its backend installp) from IBM AIX . SMIT was introduced with AIX 3.0 in 1989. Early package managers, from around 1994, had no automatic dependency resolution but could already drastically simplify

3392-432: The other variables, referred to as free , behave like ordinary first-order term variables, e.g. k ⋅ ∫ a b sin ⁡ ( k ⋅ t ) d t {\displaystyle k\cdot \int _{a}^{b}\sin(k\cdot t)\;dt} does make sense. All these operators can be viewed as taking a function rather than a value term as one of their arguments. For example,

3456-444: The previous version, as defined by the packager of the software. This process is sometimes called version pinning . For instance: Some of the more advanced package management features offer "cascading package removal", in which all packages that depend on the target package and all packages that only the target package depends on, are also removed. Although the commands are specific for every particular package manager, they are to

3520-721: The process of adding and removing software from a running system. By around 1995, beginning with CPAN , package managers began doing the work of downloading packages from a repository, automatically resolving its dependencies and installing them as needed, making it much easier to install, uninstall and update software from a system. A software package is an archive file containing a computer program as well as necessary metadata for its deployment. The computer program can be in source code that has to be compiled and built first. Package metadata include package description, package version, and dependencies (other packages that need to be installed beforehand). Package managers are charged with

3584-407: The same value in rational arithmetic . While structural equality can be checked without any knowledge about the meaning of the symbols, semantic equality cannot. If the function / is e.g. interpreted not as rational but as truncating integer division, then at n =2 the left and right term evaluates to 3 and 2, respectively. Structural equal terms need to agree in their variable names. In contrast,

3648-668: The set of (unsorted first-order) terms T is recursively defined to be the smallest set with the following properties: Using an intuitive, pseudo- grammatical notation, this is sometimes written as: The signature of the term language describes which function symbol sets F n are inhabited. Well-known examples are the unary function symbols sin , cos ∈ F 1 , and the binary function symbols +, −, ⋅, / ∈ F 2 . Ternary operations and higher-arity functions are possible but uncommon in practice. Many authors consider constant symbols as 0-ary function symbols F 0 , thus needing no special syntactic class for them. A term denotes

3712-408: The set of all terms accordingly. To this end, a sort (sometimes also called type ) is assigned to each variable and each constant symbol, and a declaration of domain sorts and range sort to each function symbol. A sorted term f ( t 1 ,..., t n ) may be composed from sorted subterms t 1 ,..., t n only if the i th subterm's sort matches the declared i th domain sort of f . Such

3776-448: The software system. They typically reside within a directory tree that is not maintained by the system-level package manager, such as c:\cygwin or /opt/sw . However, this might not be the case for the package managers that deal with programming libraries, leading to a possible conflict as both package managers may claim to "own" a file and might break upgrades. In 2016, Edgard Marx, a computer scientist from Leipzig University, coined

3840-477: The state of the local system to fall out of synchronization with the state of the package manager's database . The local administrator will be required to take additional measures, such as manually managing some dependencies or integrating the changes into the package manager. There are tools available to ensure that locally compiled packages are integrated with the package management. For distributions based on .deb and .rpm files as well as Slackware Linux, there

3904-466: The task of finding, installing, maintaining or uninstalling software packages upon the user's command. Typical functions of a package management system include: Computer systems that rely on dynamic library linking, instead of static library linking, share executable libraries of machine instructions across packages and applications. In these systems, conflicting relationships between different packages requiring different versions of libraries results in

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3968-517: The term force field , this equation defines the potential energy of the system; the force is the derivative of this potential relative to position. The meanings of right hand side terms are: The form of the van der Waals energy is calculated using the equilibrium distance ( r i j 0 {\displaystyle r_{ij}^{0}} ) and well depth ( ϵ {\displaystyle \epsilon } ). The factor of 2 {\displaystyle 2} ensures that

4032-567: The term Data Dependency Management to refer to the systems that deal with the management of data. Data Dependency Management systems are designed to facilitate the deployment and management of data on the cloud, personal computers, or smart devices (edge). Data Dependency Management frameworks can be used to describe how the data was conceived, licensing as well as its dependencies. The concept of data dependency management comes from software package dependency management tools such as npm for JavaScript, gem for Ruby, and NuGet for .NET. Their rationale

4096-732: The vector addition, the scalar multiplication, and the inner product is declared as ⁠ + : W × W → W , ∗ : W × N → W {\displaystyle +:W\times W\to W,*:W\times N\to W} ⁠ , and ⁠ ⟨ . , . ⟩ : W × W → N {\displaystyle \langle .,.\rangle :W\times W\to N} ⁠ , respectively. Assuming variable symbols v → , w → ∈ V W {\displaystyle {\vec {v}},{\vec {w}}\in V_{W}} and

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