2017 activities poster available
here 












Links to Web sites for Codes used in Molecular Simulations
General Software
FFTW web site. FFTW is a C subroutine library for computing the discrete Fourier transform (DFT)
in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete
cosine/sine transforms or DCT/DST). We believe that FFTW,
which is free software, should become the FFT library of choice for most applications.
Scientific Python
VMD, Graphics for large molecules
Other graphic packages. List.
Data Base
The Quixote Project, Data base for Quantum Chemistry calculations: Quixote is
an international collaboration heavily relying on web connectivity and voluntary work by motivated researchers.
The main objective/vision of the Quixote project is to design, test and deploy a modular, open source system of
tools that allow computational chemistry data (now sitting in the darkness of individual harddisks) to be organized,
shared, and queried. This is to be achieved by using lightweight interdependent applications, semantic analysis of the
data and linkability.
The Protein Data Bank
Classical Modeling
ESPRESSO web site. ESPResSo is a highly versatile software package
for the scientific simulation and analysis of coarsegrained atomistic or beadspring
models as they are used in soft matter research, with emphasis on charged systems.
CCP5 Software and web site Collaborative Computational Projects in Condensed Matter, inc
ludes DL_POLY Software and several other softwares.
MMTK Software and web site Molecular Modeling Tool Kit
Gromacs, Groningen Machine for Chemical Simulations
CHARMM, (Chemistry at HARvard Macromolecular Mechanics)
is a program for macromolecular simulations, including energy minimization, molecular dynamics and
Monte Carlo simulations.
Amber, "Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs);
and a package of molecular simulation programs which includes source code and demos.
NAMD, BioCore, developed by the Theoretical and Biophysics group at UrbanaChampaign
Electronic Structure
The ETSF web site. The ETSF is a knowledge center
for theoretical spectroscopy carrying out stateoftheart research on theoretical and computational
methods for studying electronic and optical properties of materials. The ETSF gathers the experience and knowhow of more than 200
researchers in Europe and the United States, facilitating collaborations and rapid knowledge transfer.
The ETSF offers its expertise to researchers, industry, and students in the form of collaborative projects,
free scientific software and training. Proposals to benefit from these services can be submitted at any moment,
and are evaluated twice a year by an external scientific panel.
ETSF suite of codes:
The Abinit web site
The dp web site
The Exc web site
The Tosca web site
The Exciting web site
The Elk web site
The APE web site
The FHI web site
The ASE web site
The GPAW web site
The fleur web site
The JACAPO web site
The TURBOMOLE web site
The SIESTA code web site. SIESTA was born in 1996 to implement,
in self consistent DFT, the orderN techniques developed for tightbinding in the early 1990s. Because orderN was
carefully imposed in all the code, this was very efficient, specially for large systems and moderate precisions. Later,
the need for higher precisions, and the addition of many new functionalities, imposed compromises to the orderN philosophy,
but efficiency kept being one of SIESTA's strongest points.
The OCTOPUS code web site. Octopus is a scientific
program aimed at the ab initio virtual experimentation on a hopefully everincreasing range of system types. Electrons
are described quantummechanically within densityfunctional theory (DFT), in its timedependent form (TDDFT) when doing
simulations in time. Nuclei are described classically as point particles. Electronnucleus interaction is described within the pseudopotential approximation.
Octopus is free software, released under the GPL license, so you are free to use it and modify it. See also the The TDDFT web site.
Quantum Espresso Quantum ESPRESSO is an integrated suite of computer codes
for electronic structure calculations and materials modeling at the nanoscale. It is based on density'functional
theory, plane waves and pseudopotentials, both normconserving and ultrasoft.
The CPMD web site Parallelized plane wavespseudopotential implementation of DFT theory.
The CP2K web site. CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic
and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g.
density functional theory (DFT) using a mixed
Gaussian and plane waves approach (GPW), and classical pair and manybody potentials.
VASP web site. VAMP/VASP is a package for performing
abinitio quantummechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set.
The approach implemented in VAMP/VASP is based on a finitetemperature localdensity approximation (with
the free energy as variational quantity) and an exact evaluation of the instantaneous electronic ground state at
each MDstep using efficient matrix diagonalization schemes and an efficient Pulay mixing.
The interaction between ions and electrons is described using ultrasoft Vanderbilt pseudopotentials (USPP) or the projector augmented wave method (PAW).
Both techniques allow a considerable reduction of the necessary number of planewaves per atom for transition metals and first row elements. Forces and stress
can be easily calculated
with VAMP/VASP and used to relax atoms into their instantaneous groundstate.
WIEN2K web site. The program package WIEN2k allows to perform electronic
structure calculations of solids using density functional theory (DFT). It is based on the fullpotential (linearized)
augmented planewave ((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. WIEN2k
is an allelectron scheme including relativistic effects and has many features.
The ADF site. The Amsterdam Density Functional software has a 30year track record as a premiumquality quantum chemistry
software package based on Density Functional Theory (DFT). It consists of the molecular DFT program ADF, the periodic DFT program BAND,
the postADF COSMORS program for thermodynamics of liquids and the ReaxFF program for modeling chemical reactions
The GAUSSIAN site Hartree'Fock and DFT quantum chemistry.
NWChem The NWChem development strategy
is focused on providing new and essential scientific capabilities to its users in the areas
of kinetics and dynamics of chemical transformations, chemistry at interfaces and in the condensed
phase, and enabling innovative and integrated research at EMSL. At the same time continued
development is needed to enable NWChem to effectively
utilize architectures of tens of petaflops and beyond.
Materials studio, by Accelerys.
Gamess US, by Mark Gordon´s group.
Gamess UK by CCP1. Both Gamess codes originate from the code written by Michel Dupuis in the 80´s. The codes have been since developed independently in the US and in the UK.


