免费的分子模拟软件（转载）
【URL】 http://www.ks.uiuc.edu/Research/namd/
【作者】 Theoretical and Computational Biophysics Group,University of Illinois at Urbana-Champaign (UIUC)
【语言版本】 English
【收费情况】 免费
【用途】 NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using switched fast ethernet. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR and is distributed free of charge with source code.
Current NAMD Feature Summary:
Software Setup
Free to download and use. (Redistribution prohibited.)
Precompiled binaries provided for 12 popular platforms.
Installed at major NSF supercomputer sites.
Portable to virtually any platform with ethernet or MPI.
C++ source code and CVS access for modification.
Molecule Building
Reads X-PLOR, CHARMM, AMBER, and GROMACS input files.
Psfgen tool generates structure and coordinate files for CHARMM force field.
Efficient conjugate gradient minimization.
Fixed atoms and harmonic restraints.
Thermal equilibration via periodic rescaling, reinitialization, or Langevin dynamics.
Basic Simulation
Constant temperature via rescaling, coupling, or Langevin dynamics.
Constant pressure via Berendsen or Langevin Nose-Hoover methods.
Particle mesh Ewald full electrostatics for periodic systems.
Symplectic multiple timestep integration.
Rigid waters and bonds to hydrogen atoms.
Advanced Simulation
Chemical and conformational free energy calculations.
Locally enhanced sampling via multiple images.
Tcl based scripting and steering forces.
Interactive visual steering interface to VMD.
Scalable Performance
Based on the Charm++/Converse parallel runtime system.
Spatial data decomposition for limited communication pattern.
Message driven execution for latency tolerance on commodity networks.
Measurement-based load balancing for scaling to hundreds of processors.
Largest simulation to date is over 300,000 atoms on 1000 processors.
2.GROMACS-GROningen MAchine for Chemical Simulations (分子动力学软件)
【URL】 http://www.gromacs.org/
【作者】 Dep. of Biophysical Chemistry, Groningen University
【语言版本】 C
【操作系统】 Unix
【下载】 http://www.gromacs.org/download/index.php
【收费情况】 免费
免费
【用途】 GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
GROMACS supports all the usual algorithms you expect from a modern molecular dynamics implementation, but there are also quite a few features that make it stand out from the competition:
* GROMACS provides extremely high performance compared to all other programs.
* GROMACS is user-friendly, with topologies and parameter files written in clear text format.
* There is no scripting language - all programs use a simple interface with command line options for input and output files.
* As the simulation is proceeding, GROMACS will continuously tell you how far it has come, and what time and date it expects to be finished.
* Both run input files and trajectories are independent of hardware endian and can thus be read by any version GROMACS, even if it was compiled using a different floating-point precision. All files from GROMACS 2.0 can further be used in the new version 3!
* GROMACS can write coordinates using lossy compression, which provides a very compact way of storing trajectory data. The accuracy can be selected by the user.
* GROMACS comes with a large selection of flexible tools for trajectory analysis - you won\'t have to write any code to perform routine analyses. The output is further provided in the form of finished Xmgr/Grace graphs, with axis labels, legends, etc. already in place!
* A basic trajectory viewer that only requires standard X libraries is included, and several external visualization tools can read the GROMACS file formats.
* GROMACS can be run in parallel, using standard MPI communication.
* GROMACS contains several state-of-the-art algorithms that make it possible to extend the time steps is simulations significantly, and thereby further enhance performance without sacrificing accuracy or detail.
* The package includes a fully automated topology builder for proteins, even multimeric structures. Building blocks are available for the 20 standard aminoacid residues as well as some modified ones, the 4 nucleotide and 4 deoxinucleotide resides, several sugars and lipids, and some special groups like hemes and several small molecules.
* There is ongoing development to extend GROMACS with interfaces both to Quantum Chemistry and Bioinformatics/databases.
【使用说明链接】 http://www.gromacs.org/documentation/index.php
3.DL_POLY (分子动力学模拟软件)
【URL】 http://www.cse.clrc.ac.uk/msi/software/DL_POLY/
【作者】 W. Smith and T.R. Forester
【语言版本】 English
【收费情况】 免费
DL_POLY is supplied to individuals under a licence and is free of cost to academic scientists pursuing scientific research of a non-commercial nature. A group licence is also available for academic research groups. All recipients of the code must first agree to the terms of the licence.
Commercial organisations interested in acquiring the package should approach Dr. W. Smith at Daresbury Laboratory in the first instance. Daresbury Laboratory is the sole centre for distribution of the package.
【用途】 DL_POLY is a general purpose serial and parallel molecular dynamics simulation package originally developed at Daresbury Laboratory by W. Smith and T.R. Forester under the auspices of the Engineering and Physical Sciences Research Council (EPSRC) for the EPSRC\'s Collaborative Computational Project for the Computer Simulation of Condensed Phases (CCP5) and the Molecular Simulation Group (MSG) at Daresbury Laboratory. The package is the property of the Central Laboratory of the Research Councils.
Two versions of DL_POLY are currently available. DL_POLY_2 is the original version which has been parallelised using the Replicated Data strategy and is useful for simulations of up to 30,000 atoms on 100 processors. DL_POLY_3 is a version which uses Domain Decomposition to achieve parallelism and is suitable for simulations of order 1 million atoms on 8-1024 processors.
4.并行分子动力学模拟软件DoD-TBMD
【URL】 http://cst-www.nrl.navy.mil/~mehl/tbmd/
【作者】 Florian Kirchhoff
【语言版本】 English
【收费情况】 免费
【用途】 DoD-TBMD is a code for doing molecular dynamics simulations of metallic systems. It uses a quantum-mechanical description of the inter-atomic interactions. The Hamiltonian of the system is approximated using an empirical tight-binding model. The electronic-structure is calculated either by direct diagonalization or by using an O(N2) method called the Kernel Polynomial Method (KPM). The code has been written for both scalar and parallel computers. The parallel parts of the code have been written using a message-passing programming model relying on the MPI library to deal with communications.
【备注】
If you have any comments, suggestions or questions
send Florian Kirchhoff an e-mail at kirchhoff.5@osu.edu (Privacy Advisory)
5.蛋白质分子动力学模拟软件：CONCOORD
【URL】 http://www.mpibpc.gwdg.de/abteilungen/071/bgroot/concoord.html
【作者】 Bert de Groot
【语言版本】 C
【操作系统】 Unix/Linux
【收费情况】 免费
【用途】 CONCOORD is a method to generate protein conformations around a known structure based on distance restrictions. Principal component analyses of Molecular Dynamics (MD) simulations of proteins have indicated that collective degrees of freedom dominate protein conformational fluctuations. These large-scale collective motions have been shown essential to protein function in a number of cases. The notion that internal constraints and other configurational barriers restrict protein dynamics to a limited number of collective degrees of freedom has led to the design of the CONCOORD method to predict these modes without doing explicit, more CPU intensive, MD simulations.
Methodology
The CONCOORD method consists of two stages. The first stage is the identification of all interatomic interactions in the starting structure. These interactions are divided among different categories, depending on the strength of the interaction. Covalent bonds form the tightest interactions and long-range non-bonded interactions are among the weakest interactions. Based on the strength of the interaction, a specific distance freedom is given to each interacting pair. In this way, a set of upper and lower distance bounds is obtained for all interacting pairs of atoms. The second stage consists of generating structures other than the starting structure that fulfill all distance bounds. This is achieved by iteratively applying corrections to randomly generated coordinates untill all distance bounds are fulfilled.
Software
The CONCOORD software consists of two programs, one for each stage. The program dist generates the distance bounds and disco is the program that generates structures from these bounds. These two programs will be put in the PATH environment variable by sourcing the CONCOORDRC file in the CONCOORD root directory. Additionally, the location of a number of library files will from then on also be known to the programs. An interface to CONCOORD can be found in the WHAT IF package.
【使用说明】
This is the information you get when using the -h option:
dist:
Usage: dist -g (or -p ) [-dssp ]
[-r] [-nb] [-c value] [-m value]
[-op ] [-og ] [-od ] [-h]
dist sorts pairs of interacting atoms in a (protein) structure from a single conformation. The result can be used by the program disco to generate multiple conformations.
disco:
Usage: disco [-d ] [-p ] [-n value] [-i value] [-r ]
-op (or -ox or -ot ) [-or ]
[-of ] [-c ] [-bs ] [-s ] [-f] [-v] [-h]
disco generates a number of protein conformations based on a set of interatomic distance constraints (usually generated by the program dist, but also additional restraints may be specified).
【备注】
The software is distributed with NO WARRANTY OF ANY KIND. The author is not responsible for any losses or damages suffered directly or indirectly from the use of the software. Use it at your own risk.
Reference
If you publish CONCOORD results, please cite:
B.L. de Groot, D.M.F. van Aalten, R.M. Scheek, A. Amadei, G. Vriend and H.J.C. Berendsen; "Prediction of protein conformational freedom from distance constraints", PROTEINS: Struct. Funct. Gen. 29: 240-251 (1997) [pdf]
Send your bug reports, comments and suggestions to:
bgroot@gwdg.de.
6.Virtual Molecular Dynamics Laboratory (分子动力学软件)
【URL】 http://polymer.bu.edu/vmdl/index.html
【作者】 Amit Bansil, Lidia Braunstein
【语言版本】 English
【收费情况】 免费
【用途】 The Virtual Molecular Dynamics Laboratory enables the student to visualize atomic motion, manipulate atomic interactions, and quantitatively investigate the resulting macroscopic properties of biological, chemical, and physical systems.
The Virtual Laboratory is a suite of research-based molecular dynamics software tools and project-based curriculum guides. The software tools are: "Simple Molecular Dynamics (SMD)", "Universal Molecular Dynamics", and "Water".
7.AL_CMD 美国能源部Ames实验室经典分子动力学软件
【URL】 http://cmp.ameslab.gov/cmp/CMP_Theory/cmd/alcmd_source.html
【作者】 Dave Turner, Jamie Morris
【语言版本】 English
【系统配置要求】 Intel Paragon, nCube 2S, IBM SP-2, scalar computers
【收费情况】 免费
【用途】 This code is provided to the general public by Ames Laboratory, as part of the HPCC Materials Science Grand Challenge project of the U.S. Department of Energy. A spatial decomposition approach enables it to run efficiently on a wide variety of computers including the Intel Paragon, nCube 2S, IBM SP-2, scalar computers, or any parallel computer that utilizes the MPI communications library. A variety of classical atomic interactions are supported including simple Leonard-Jones pair interactions, the Embedded-Atom Method, and 3-body interactions using Tersoff potentials.
【备注】
All researchers utilizing this code should acknowledge Ames Laboratory and the U.S. Department of Energy in any published work, and email them a citation on where it was published.
turner@ameslab.gov
or
jrmorris@ameslab.gov.
8.ProtoMol (分子动力学并行计算软件)
【URL】 http://www.nd.edu/~lcls/Protomol.html
【作者】 LCLS Group at the University of Notre Dame
【语言版本】 English
【操作系统】 SunOS 5.8, IRIX 6.5, Linux 2.4, AIX 5.1
【收费情况】 免费
【用途】 PROTOMOL is an object-oriented component based framework for molecular dynamics simulations. The framework supports the CHARMM 19 and 28a2 force fields and is able to process PDB, PSF, XYZ and DCD trajectory files. It is designed for high flexibility, easy extendibility and maintenance, and high performance demands, including parallelization. The technique of multiple time-stepping has been used to improve long-term efficiency, and the use of fast electrostatic force evaluation algorithms like plain Ewald, Particle Mesh Ewald, and Multigrid summation further improves performance. Longer time steps are possible using MOLLY, Langevin Molly and Hybrid Monte Carlo, Nose-Hoover, and Langevin integrators. In addition, PROTOMOL has been designed to interact with VMD, a visualization engine developed by the University of Illinois that is used for displaying large biomolecular systems in three dimensions. PROTOMOL is free distributed software, and the source code is in cluded.
9.PAPA (计算粒状物料的三维并行分子动力学计算程序)
【URL】 http://www.ica1.uni-stuttgart.de/Research/Software_P3T/papa.html
【作者】 ICA 1 Group, Institute of Computer Applications (ICA) of the University of Stuttgart
【语言版本】 English
【收费情况】 免费
【用途】 Characteristic:
dissipative interaction for rotating, rough, spherical particles
geometry elements: walls, cylinders, spheres, etc freely configurable
material properties of walls and particles freely configurable for an arbitray number of materials
object oriented, written in C++
full checkpointing supported
several compilation options: support of X11 graphics, reduction to 2D, debugging aids, etc.
Applications:
simulation of granular media, silo filling and steady flow problems, sphere packings of mono- and polydisperse system
10.ORAC (用于模拟溶剂化生物分子的分子动力学计算程序, 意大利佛罗伦萨大学)
【URL】 http://www.chim.unifi.it/orac/
【作者】 Massimo Marchi and P. Procacci
【语言版本】 English
【操作系统】 UNIX
【收费情况】 免费
【用途】 ORAC is a program for running classical simulations of biomolecules. Simulations can be carried out in the NVE, NPT, NHP, and NVT thermodynamic ensembles. The integration of the equations of motion in any ensemble can be carried out with the r-RESPA multiple time step integrator and electrostatic interactions can be handled with the Smooth Particle Mesh Ewald method.
【备注】
A parallel version of ORAC4.0 (MPI/T3E) is available upon request to:
Massimo Marchi
Section de Biophysique des Proteines et des Membranes,
DBCM, DSV, CEA, Centre d\'Etudes,
Saclay, 91191 Gif-sur-Yvette Cedex, FRANCE
11.MDynaMix (分子动力学计算软件)
【URL】 http://www.fos.su.se/physical/sasha/md_prog.html
【作者】 Alexander Lyubartsev
【语言版本】 English
【操作系统】 PC-Pentium (PPro,PII) Linux 2.0 and more
【收费情况】 免费
【用途】 This is a general purpose molecular dynamics code for simulations of mixtures of either rigid or flexible molecules, interacting by AMBER-like force field in a periodic rectangular cell. In the case of flexible molecules the double time step algorithm is used. Algorithms for NVE, NVT and NPT statistical ensembles are employed, as well as optimized Ewald sum for treatment of the electrostatic interactions. The program can be run both in sequential and parallel execution. The parallel version employes "replicated data" strategy. It can be run on any parallel architecture or workstation cluster with MPI parallel environment installed.
This program was originally based on the MOLDYN program by Aatto Laaksonen available from the CCP5 program library , Daresbury Lab, UK. Since 1993 many additional changes were made by Alexander Lyubartsev, some of these are:
NVT ensemble (v2.1)
NPT ensemble (v3.0)
complex DNA-like molecules (v3.5)
non-cubic (rectangular) cell, optimized Evald sum calculation (v3.6)
hydrogen bonds included (10-12 potential) (v3.7)
first parallel version (v3.8)
fully parallelized code (v4.0)
several types of dihedral angles potentials, Morse bond potential (v.4.1) New (free) format of input data.
option for separate pressure controll in each direction; reaction field method method for the electrostatic interactions; options for truncated octahedron or hexagonal simulation cell (v4.2)
explicit reversible integrator for NPT-dynamics (Martyna et all, J.Chem.Phys, 101, 4177 (1994) is implemented; option for ASCII format of the restart file; some other options; more comments in the source files (v.4.3); utility "makemol" for easier constructing of molecular models is added
12.MDRANGE (分子动力学计算ion ranges)
【URL】 http://beam.helsinki.fi/~knordlun/mdh/mdh_program.html
【作者】 Kai Nordlund
【语言版本】 English
【收费情况】 免费
【用途】 The official name of the program is MDRANGE. However, in the actual program files the shorter, more convenient name mdh (abbreviated from Molecular Dynamics High-energy) is used. Both names therefore (at least for now) mean exactly the same program. The program is a molecular dynamics (MD) simulation program tailored for effective calculation of ion ranges. The word effective used here must be understood in the context of high-energy molecular dynamics calculations.
What it does
Calculates ion ranges in solids
Calculates deposited energies
Calculates the primary recoil spectrum
Obtaining stopping powers possible indirectly
Ion and sample elements which can be used: any
Energy range in which calculation can be done: roughly 1 eV/amu - 10 MeV/amu
Energy range in which use is justified: roughly 100 eV/amu - 100 keV/amu
MDRANGE3.0: option for Puska-Echenique-Nieminen-Ritchie(PENR)-electronic stopping model [Sil00]. Needs charge density file from user.
MDRANGE3.0: option for Brandt-Kitakawa(BK)-electronic stopping model. Needs charge density file from user.
【备注】
Kai Nordlund
Accelerator Laboratory, University of Helsinki, P.O. BOX 43, FIN-00014 Helsinki, Finland
(email kai.nordlund@helsinki.fi)
13.GROMOS (通用分子动力学软件包)
【URL】 http://www.igc.ethz.ch/gromos/
【作者】 Laboratory of Physical Chemistry,ETH
【语言版本】 English
【收费情况】 部分免费
free for academics
This means that GROMOS96 is available for non-commercial institutes at the price of US $ 400,- which is meant to cover costs of administration (manual, correction letters, etc.) and distribution medium handling. For this amount, help with installation of GROMOS or familiarization with it cannot be expected. Industry has to pay substantially more for GROMOS (US $ 12000.-, additional information)
【用途】 GROMOS is a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems. Its purpose is threefold:
a. Simulation of arbitrary molecules in solution or crystalline state by the method of molecular dynamics (MD), stochastic dynamics (SD) or the path-integral method.
b. Energy minimisation of arbitrary molecules.
c. Analysis of conformations obtained by experiment or by computer
simulation.
The simulation package comes with the GROMOS force field (proteins, nucleotides, sugars, etc.) the quality of which should be judged from the scientific literature concerning its application to chemical and physical systems, ranging from glasses and liquid crystals to polymers and crystals and solutions of biomolecules.
【备注】
free for academics
14.DPD应用软件cerius2
【URL】 http://www.accelrys.com/cerius2/dpd.html
【作者】 Accelrys Inc.
【语言版本】 English
【操作系统】 Unix
【系统配置要求】 SGI IRIX 工作站和IBM工作站
【收费情况】 免费
Accelrys European Headquarters
230/250 The Quorum, Barnwell Road
Cambridge, CB5 8RE, UK
Tel: +44 1223 413300
Accelrys Corporate Headquarters
9685 Scranton Road
San Diego, CA 92121-3752, USA
Tel: +1 858 799 5000
Accelrys Asia Headquarters
Nakarin - Auto Building SF,
2-8-4 Shinkawa,
Chuo-ku, Tokyo 104-0003, Japan
Tel: +81 3 3206 3575
A subsidiary of Pharmacopeia Inc.
【用途】 C2·DPD (Dissipative Particle Dynamics) is a novel mesoscale simulation method for studying flows in complex fluids, such as suspensions, emulsions and polymer melts。
The following features are available in the Cerius2 DPD module:
The user can choose the number density and temperature of the system.
The user can vary details of the interaction strengths between beads. These are related to the fluid equation of state, and are a function of the colours of the particles i and j in the case of a binary fluid. These are essentially the Flory-Huggins parameters of the system.
The user can connect some of the particles by bonds, which are harmonic springs with a variable spring constant. These represent the statistical behaviour of a Kuhn segment of a polymer. Polymers can be branched.
"Sliding Brick" boundary conditions for imposing an external shear will be enabled, as will solid surfaces, with user-definable values of the surface interaction parameters.
The user can output conformational information regarding bonded groups (e.g., radius of gyration), and to visualise average particle density fields.
【使用说明链接】 http://www.accelrys.com/doc/materials/cerius40/proppred/dpd.doc.html#139873
15.CHARMM (大分子分子力学模拟计算软件)
【URL】 http://yuri.harvard.edu/
【作者】 the research group of Professor Martin Karplus at Harvard University
【语言版本】 English
【收费情况】 部分免费
The source code of the CHARMM program with documentation is distributed to individual academic research groups for a $600 licensing fee. CHARMM runs on a variety of UNIX workstations, including the SG Indigo machines. No graphics are necessary.
【用途】 CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a program for macromolecular dynamics and mechanics. It performs standard molecular dynamics in many different ensembles (e.g., NVE, NVT, NPT) using state-of-the-art algorithms for timestepping, long range force calculation and periodic images. CHARMM can be used for energy minimization, normal modes and crystal optimizations as well. The potential energy functions available for use with CHARMM have been extensively parameterized for simulations of proteins, nucleic acids and lipids. Free energy methods for chemical and conformational free energy calculations are also fully developed and available in CHARMM. Many other novel tools have been developed and are available in CHARMM, these include: replicas (multiple copies); many types of restraints and constraints, including fixed atoms, atomic, NOE, dihedral and internal coordinate restraints and generalized SHAKE for bonds and arbitrary internal coordina tes; minimium energy path following and transition state optimization; etc.
【备注】
Professor Martin Karplus
Department of Chemistry & Chemical Biology
12 Oxford Street
Harvard University
Cambridge, Massachusetts 02138
16.免费远程计算：贵州大学GHPCC量子化学从头计算系统
【URL】 http://ghpcc.gzu.edu.cn/
【收费情况】 免费
【用途】GHPCC远程开放量子化学从头计算系统，可提供完下列免费的化学计算:
*Hartree-Fock
*密度泛函DFT
*Moller-Plesset微扰理论计算
*半经验量子化学计算
GHPCC 现提供出一套8节点PIII并行计算系统给国内量化计算同仁免费使用
计算软件升级为GaussNet 2000/Parallel
整体并行计算速度为原来的 5倍（半经验方法不支持并行计算，仍为串行计算）
能同时运行的并行作业数放大到 4个
将提供更丰富的密度泛函、基函数，计算类型如：TS优化、FREQ计算等
下一步GHPCC将挂接和调试MPQC高性能并行量化程序，作为后台支持计算系统
【用户输入】 在线填写有关表格，按照提示提交操作。
【使用说明】
在线帮助包括以下内容，请自行查阅。
*系统功能与执行流程
*计算过程图例
*常见问题及回答
*Gaussian On-line Help
【备注】
本系统为不关机系统，在网络通讯正常的任何时刻均可使用。国外IP地址的机器不能访问使用。
17.SURFNET (量子化学计算程序)
【URL】 http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html
【作者】 Roman A Laskowski
【系统配置要求】 The SURFNET program generates surfaces and void regions between surfaces from coordinate data supplied in a PDB file
【收费情况】 免费
【用途】 It can compute:
van der Waals surfaces
Gaps between molecules
Clefts, cavities and binding sites
3D density distributions and sidechain-sidechain interactions
Planes, paraboloids and boxes
【备注】
Available free to academic institutions by anonymous ftp on: http://www.cnblogs.com/animam_effla/admin/ftp://ftp.biochem.ucl.ac.uk/
18.PSI3量子化学软件包(量化从头计算)
【URL】 http://www.psicode.org/psi3.html
【下载】 http://www.psicode.org/downloads.php
【系统配置要求】 PSI3 is designed for use on a variety of UNIX-based systems. The package has been tested in the following environments:
【收费情况】 免费
【用途】 PSI3 suite of quantum chemical programs is designed for efficient, high-accuracy calculations of properties of small to medium-sized molecules. The package\'s current capabilities include a variety of Hartree-Fock, coupled cluster, complete-active-space self-consistent-field, and multi-reference configuration interaction models. Molecular point-group symmetry is utilized throughout to maximize efficiency.
【使用说明】
The latest version of the code, PSI 3.2, rests upon a completely rewritten infrastructure relative to previous versions of the package. Non-standard computations are possible using a customizable input format.
The latest version of the PSI3 package is psi-3.2-rc2, which was uploaded on 19 November 2003. PSI3 is distributed under the terms of the GNU General Public License (GPL). This means that the program is free software with NO WARRANTY, either expressed or implied, as to its performance or correctness.
Primary development on PSI3 has been carried out by:
Prof. T. Daniel Crawford (Virginia Tech)
Prof. C. David Sherrill (Georgia Tech)
Dr. Edward F. Valeev (Georgia Tech)
Prof. Rollin A. King (Bethel College)
19.CADPAC (剑桥量子化学计算软件)
【URL】 http://www-theor.ch.cam.ac.uk/software/cadpac.html
【收费情况】 免费
【用途】 Briefly the main capabilities are as follows,
(a) The evaluation of 1 and 2-electron integrals over contracted cartesian gaussian basis functions of type s, p , d , or f. The program can also use pseudopotentials of both the Huzinaga and the Hay-Wadt forms.
(b) SCF energy calculations for closed shell, open-shell, UHF and generalised open-shell techniques. The algorithms used can be either \'in core\', or conventional or \'direct\' according to the size of the calculation.
(c) calculation of 1-electron properties, including distributed multipoles.
(d) calculation of the gradients of the SCF energy.
(e) use of the gradients for automatic geometry optimization, the location of saddle points and for the calculation of force constants by numerical differentiation. There is a choice of two optimization algorithms.
(f) transformation of the integrals from the atomic orbital to the molecular orbital basis. A \'semi-direct\' transformation exists for large cases.
(g) Moller-Plesset perturbation theory calculations to fourth order in the energy and second order in the 1-electron properties. The Moller-Plesset routines are closed-shell, UHF or ROHF. The second-order routines can be conventional or direct.
(h) coupled Hartree-Fock calculations of polarizabilities, including the frequency dependence, excitation energies, magnetizabilities and nmr shielding constants.
(i) coupled Hartree-Fock calculations of the perturbation due to nuclear displacements.
(j) calculation of the dipole and quadrupole moment derivatives.
(k) calculation of the second derivatives ( force constants) of the energy by analytic methods.
(l) analytic calculations of polarizability derivatives.
(m) calculation of infrared and Raman intensities, and the study of vibrational circular dichroism.
(n) calculation of MP2 gradients, dipole moment derivatives, polarizabilities and force constants using analytic algorithms.
(o) spin-projected UHF MP2 energies
(p) frequency dependent hyperpolarisabilities.
(q) a variety of CI and coupled-cluster based methods.
(r) a variety of density functional methods, both closed-shell and open-shell, and including analytic gradients and force constants, and nmr shielding. The functionals available included local density and gradient corrected methods, and functionals with partial SCF exchange.
(s) calculation of distributed multipoles and polarisabilities by numerical integration.
(t) Intermolecular perturbation theory.
(u) Finite field calculations using external fields, field gradients and lattices.
【使用说明】
The Cambridge Analytic Derivatives Package (CADPAC) is a suite of an ab initio molecular orbita programs which has been under development at Cambridge since 1981. It is available for downloading for a limited period only. Documentation including a searchable index is available online.
Contact
Email: cadpac@theor.ch.cam.ac.uk
20.WebMO (基于3W界面的计算化学软件包)
【URL】 http://www.webmo.net/
【系统配置要求】 unix or Linux system.
【收费情况】 免费
【使用说明】
Here are some key features of WebMO:
Users draw structures in a 3D java editor, run calculations, and view results, all from their web browser
All administrative tasks (user accounts, job time limits, etc) are performed through a web browser interface
No software to install on the client. WebMO is installed only on the single web server that runs the computational chemistry programs
Simple enough for undergraduate computational chemistry curriculum
Flexible enough for computational chemistry research
Support for Gaussian 94, Gaussian 98, MOPAC, MOPAC 2000, and GAMESS
Fragment library to speed up entry of large or complex molecules
Import existing XYZ, MOL or PDB structures directly into the editor
Works fully with Netscape 4.07+ (PC, unix), IE 4.0+ (PC, unix), and HotJava 3.0+ (PC, Macintosh)
【备注】
WebMO is a World Wide Web-based interface to computational chemistry packages. WebMO is available for free and can be installed on nearly any unix or Linux system.
Contact
WebMO, LLC
mailto:webmo@webmo.net
21.AMSOL (半经验量子化学计算)
【URL】 http://t1.chem.umn.edu/amsol/
【收费情况】 免费
【使用说明】
AMSOL available from the University of Minnesota is an SCF program with unique capabilities for calculating free energies of solvation of molecules and ions in solution and for calculating class IV partial atomic charges. The solvation models and charge models are based on NDDO semiempirical molecular orbital theory in which the terms required to calculate the free energy of solvation are included in the solute Hamiltonian. AMSOL employs either the AM1, PM3, or MNDO model for the solute electronic Hamiltonian. The web supplies recent revision history
, program description, abstract and manual as well as links to related websites.
contact
James W Hildebrand
Assistant Director Univ Wide
Patents/Technology Marketing
Patents and Technology Mktg
450 McNamara Center
200 Oak Street SE
Minneapolis, MN 55455
Office Phone: +1 612-624-9568
Fax: +1 612-624-6554
hilde017@umn.edu