High performance gpuaccelerated ab initio molecular dynamics and tddft software package for very large molecular or even nanoscale systems. Computer programs for the multipole electrostatics and reaction field have been incorporated into the tinker molecular modeling package developed in the ponder lab. Tinkerhp is an evolution of the popular tinker package that conserves it simplicity of use but brings new capabilities allowing performing very long molecular dynamics simulations on. It will remove the heteroatoms such as ligand, which you can use poltype to generate parameters for. Molecular buildereditor for windows, linux, and mac os x. Citeseerx document details isaac councill, lee giles, pradeep teregowda. Tinker is designed to be an easily used and flexible system of programs and routines for molecular. The tinker software, currently released as version 8, is a modular molecular mechanics and dynamics package written primarily in a standard, easily portable dialect of fortran 95 with openmp extensions. Tinker hp is an evolution of the popular tinker package that conserves it simplicity of use but brings new capabilities allowing performing very long molecular dynamics simulations on. Welcome to the section dedicated to tinker, a freeware molecular modeling package to perform molecular mechanics mm and molecular dynamics md calculations developed at jay ponders lab.
In tinker params, you can find preexisting parameters for certain molecular systems, both amoeba, amber, charmm, opls, mmff, and mm23. Tinker is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. Qchem is available a standalone package with a fully integrated graphic interface iqmol. It supports a wide variety of force fields, including polarizable models such as the atomic multipole optimized energetics for biomolecular applications amoeba force.
Avogadro free crossplatform molecular editor avogadro. Tinker has the ability to use any of several common parameter sets, such as amber ff94, ff96, ff98 and ff99, charmm 19 and 27, allinger mm mm21991 and mm32000, opls oplsua, oplsaa. Vmd can be used to display the results of hole calculations. Tinker for linux has the ability to use any of several. There are binary files for linux 32bit and 64bit, mac os x and windows 32bit and 64bit. Avogadro is an advanced molecule editor and visualizer designed for crossplatform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. The csa is incorporated into the tinker molecular modeling package along with a bspline method for capri round 5 experiments. Provides functions for molecular mechanics and dynamics, with some features for.
It supports a wide variety of force fields, including polarizable models such as the atomic multipole optimized energetics for biomolecular applications amoeba force field. Here we extend the above software list by presenting a driver for replicaexchange simulations with the tinker molecular modeling package. I yes yes yes yes i i yes yes software tools for molecular design tinker. Unlike most of the software ive covered in this space, tinker isnt available in the package systems of most distributions. Molecular and biomolecular structures can be downloaded from the pubchem, ncbi and pdb databases. The tinker molecular modeling research software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. Pros cons easy to use serial code only many readytouse force. Eventually we will deploy a less monolithic document with additional features such as sorting and filtering, correct citations, and a better layout. Raising the performance of the tinkerhp molecular modeling.
Tinker software tools for molecular design jay ponder. Sep 14, 2019 of the tinker hp molecular modeling package. We focus here on the reference, double precision, massively parallel molecular dynamics engine present in tinkerhp and dedicated to perform large scale simulations. Integration of ligand field molecular mechanics in tinker. This collection focuses on the tools available at imperial college and also on software which is predominantly free or low cost. Raising the performance of the tinkerhp molecular modeling package on intels hpc architectures. This reaction field method scales linearly with the size of the system, allowing longrange electrostatic effects to be considered with little computational expense. The full distribution is available for download via the links below in two different compressed formats gnu gzip and windows zip. May 17, 2015 lecture at the university of sao paulo molecular modeling. Program for bio molecular modeling, particularly for molecular graphics and dynamics with implicit and explicit water models. Molecular modelling software the following represents a brief collection of software tools developed for molecular modelling and visualisation. We present an order n method for calculating electrostatic interactions that has been integrated into the molecular dynamics portion of the tinker molecular modeling package.
The tinker molecular modelling software is a general package for molecular mechanics and dynamics, with some special features for biopolymers, written by professor jay ponder washington university in st louis. The tinker molecular modeling package represents a complete set of. We focus here on the reference, double precision, massively parallel molecular dynamics engine present in tinker hp and dedicated to perform large. We show how it can be adapted to recent intel central processing unit cpu petascale architectures.
Tinker is a complete package for performing empirical force field molecular mechanics and. Tinkerhp is an evolution of the popular tinker package code that conserves it most popular 20182019 physical and theoretical. Tinker employs an implementation of atomic multipolebased electrostatics with explicit dipole polarizability. It provides the most common methods in molecular simulations molecular dynamics, energy minimization, normal mode analysis and several force fields used for biomolecules amber 94, amber 99, several elastic network models. Vmd is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3d graphics and builtin scripting. They were obtained using the tinker molecular modeling package 30. This is a large download which contains the code for all components, including the java source for ffe itself and the many. The tinker molecular modeling software is a free complete and general package for molecular mechanics and dynamics, with some special features for polypeptides. Tinkerhp is a cpu based, double precision, mpi massively parallel package dedicated to long polarizable molecular dynamics simulations and to polarizable qmmm.
It is a free, opensource software that was written and is maintained by professor j. Tinker hp is a cpu based, double precision, mpi massively parallel package dedicated to long polarizable molecular dynamics simulations and to polarizable qmmm. Tinker with molecular dynamics for fun and profit linux journal. Ponder, pengyu ren, jeanphilip piquemal chemical physics, computational physics, computer science, intel xeon phi, mathematical software, molecular dynamics. Provides functions for molecular mechanics and dynamics, with some features for biopolymers.
The tinker molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. We present tinkerhp, a massively mpi parallel package dedicated to classical molecular dynamics md and to multiscale simulations, using advanced polarizable force fields pff encompassing distributed multipoles electrostatics. The core of the package is a modular set of callable routines which allow manipulating coordinates and evaluating. Tinker has the ability to use any of several common parameter sets, such as amber95, charmm22, mm21991, mm32000, oplsaa and oplsua. Tinker is a free molecular modeling package for molecular mechanics and molecular dynamics simulations. Tinker has the ability to use any of several common parameter sets, such. This software is indispensable to fmo fragment molecular orbital method of gamess.
Generally speaking, the tinker molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. The tinkerffe package runs on linux, macintosh and windows systems. Vmd can also load tinker archive file containing many structures, used for md trajectory and movies etc. Tinker is designed to be an easily used and flexible system of programs and routines for molecular mechanics and dynamics as well as other energybased and structural manipulation calculations. It offers flexible high quality rendering and a powerful plugin architecture. Introduction to the tinker package goodman group university. Tinker, stylized as tinker, is a computer software application for molecular dynamics simulation with a complete and general package for molecular mechanics and molecular dynamics, with some special features for biopolymers. I am new to linux and to this program and was wondering if anyone here could help me. I yes yes yes yes i i yes yes software tools for molecular designtinker. Open source molecular modeling about open source molecular modeling here we maintain an updateable catalog of open source molecular modeling software, initially taken from our paper.
In tinkerparams, you can find preexisting parameters for certain molecular systems, both amoeba, amber, charmm, opls, mmff, and mm23. In the table below, i have tried to summarize what i think the pros and the cons of tinker are. This page is my personal wiki of tinker, it is not the official wiki of tinker, nor it is related in anyway with tinker. Program focused on molecular dynamics of biopolymers. This means you will have to go out and download it from the main web site. We focus here on the reference, double precision, massively. More movies on molecular modeling are available at the youtube channel molecular modeling tutorial. Pdf raising the performance of the tinkerhp molecular. The latest addition to wavefunctions line of molecular modeling software for research and education. It can be obtained from the tinker webpage both as source code and as prebuilt binaries for windows, linux and mac os x. Tinker for linux 64 bit is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. I am new to linux and to this program and was wondering if anyone here could help me troubleshoot or help me find a place that will help me troubleshoot.
Runs on nvidia gpus and 64bit linux, has heavily optimized cuda code. Abstract we apply conformational space annealing csa, an efficient global optimization method, to the study of proteinprotein interaction. Tinker, stylized as tinker, is a computer software application for molecular dynamics simulation with a complete and general package for molecular mechanics. Tinker has the ability to use any of several common parameter sets, such as amber ff94, ff96, ff98, ff99, ff99sb, charmm 19, 22, 22cmap, allinger mm. The tinker molecular modeling software is a complete and general package for molecular mechanics and dynamics. Download wikidust or script editor versions of tinkercell wikidust editor is a program for drawing and uploading the diagrams to wiki sites wikidust editor windows installer. Ponder, pengyu ren, jeanphilip piquemal chemical physics, computational physics, computer science, intel xeon phi, mathematical software, molecular dynamics, molecular modeling, openmp, package. Cai, an imagebased reaction field method for electrostatic interactions in molecular dynamics simulations of.
Any opinions, findings, and conclusions or recommendations expressed in the tinker molecular modeling package are those of the authors and do not reflect the views of either the national science foundation or the national institutes of health. We show how it can be adapted to recent intel central processing unit. The ligand field molecular mechanics lfmm method for transitionmetal complexes has been integrated in tinker, an easily available and popular molecular modeling software package. There are binary files for linux 32bit and 64bit, mac os x. We focus here on the reference, double precision, massively parallel molecular dynamics engine present in tinker hp and dedicated to perform large scale simulations. Calculations for the models spce 21, tip5p 23, tip3f 24 and amoeba 25 give. The molecular modeling toolkit mmtk is a library for molecular simulation applications. Vmd supports computers running macos x, unix, or windows, is distributed free of charge, and includes source code. The tinker molecular modelling software is a general package for molecular mechanics and dynamics, with some special features for biopolymers, written by professor jay ponder washington university in st louis it should be cited as.
Jan 01, 20 generally speaking, the tinker molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. Scigress scigress is a unique desktop molecular modeling software package that can apply a wide range of computational models to all types of molecular systems, from small organic molecules, to inorganics, polymers, materials systems and whole proteins. The core of the package is a modular set of callable routines which allow manipulating coordinates and evaluating potential energy and derivatives. Once loaded, press the arrow buttons at the bottom of vmd main window to play the movie. Tinker offers access to more than a dozen empirical potentials including amoeba, one of the more elaborate polarizable atomic multipolebased potentials, as well as a wide range of solvent models. We focus here on the reference, double precision, massively parallel molecular dynamics engine present in tinkerhp and dedicated to perform large. The capability to calculate lfmm potentials has been provided by extending the functional forms of the tinker package as well as by integrating routines for calculating the ligand field. The tinker molecular modeling software is a complete and general package for. Comparison of software for molecular mechanics modeling. A molecular modeling software package, tinker 11, is used in stcsb to prepare a direct input file for md or 3drism calculations. Scigress speeds timetodiscovery by providing powerful computing and analytical tools. Facio is named after a latin verb facio which means i make. Proprietary, trial licenses available petachem llc.
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