E-CAM News

  • QQ-Interface (Quantics-QChem-Interface)

    QQ-Interface (Quantics-QChem-Interface)

      The QQ-Interface module connects the full quantum nonadiabatic wavefunction propagation code Quantics to the time-dependent density functional theory (TDDFT) module of the electronic structure program Q-Chem. Q-Chem provides analytic gradients, Hessians and derivative couplings at TDDFT level. With this module, it is possible to use the Q-Chem TDDFT module for excited state direct …Read More »
  • New publication is out: “Unimolecular FRET Sensors: Simple Linker Designs and Properties”

    New publication is out: “Unimolecular FRET Sensors: Simple Linker Designs and Properties”

      A new publication by researchers at University College Dublin and Boston University including E-CAM funded corresponding author Dr. Donal MacKernan was published in Nano Communication Networks. The measurement of biomarkers and ligands are increasingly used to study transport, signaling, and communication in cells, and as diagnostics/prognostics of disease, or the …Read More »
  • PLUMED wrapper for OpenPathSampling

    PLUMED wrapper for OpenPathSampling

      PLUMED is a widely used and versatile rare-event sampling and analysis code that can be used with various Molecular Dynamics (MD) engines. It has a very intuitive and versatile syntax for the definition of Collective Variables (CVs), and a wide variety of sampling methods, which accounts for its widespread use. …Read More »
  • The Curse of Dimensionality in Data-Intensive Modeling in Medicine, Biology, and Diagnostics

    The Curse of Dimensionality in Data-Intensive Modeling in Medicine, Biology, and Diagnostics

    With Prof. Tim Conrad (TC), Free University of Berlin, and Dr. Donal Mackernan (DM), University College Dublin. Abstract Until recently the idea that methods rooted in statistical physics could be used to elucidate phenomena and underlying mechanisms in biology and medicine was widely considered to be a distant dream.  Elements …Read More »
  • Scientific reports from the 2018 E-CAM workshops are now available on our website

    Scientific reports from the 2018 E-CAM workshops are now available on our website

      The scientific reports* from the following workshops conducted in year 3 of the project E-CAM (2018): E-CAM Scoping Workshop: “Solubility prediction”, 14 – 15 May 2018, Ecole Normale Supérieure de Lyon, France, E-CAM Scoping Workshop: “Dissipative particle dynamics: Where do we stand on predictive application?”, 24 – 26 April …Read More »
  • Improving I/O of DL_MESO_DPD files using SIONlib

    Improving I/O of DL_MESO_DPD files using SIONlib

      This module implements the SIONlib library to optimize the I/O (writing/reading) of the trajectory files generated by DL_MESO_DPD, the Dissipative Particle Dynamics (DPD) code from the DL_MESO package. SIONlib is a library for writing and reading binary data to/from several thousands of processors into one or a small number …Read More »
  • PaPIM: A code for Quantum Time Correlation Functions

    PaPIM: A code for Quantum Time Correlation Functions

      PaPIM code is a package to study the (quantum) properties of materials, and in particular time correlation functions, via the so-called mixed quantum-classical methods. In these schemes, quantum evolution is approximated by appropriately combining a set of classical trajectories for the system. Several quantum effects, for example, the possibility …Read More »
  • E-CAM Case Study: Designing control pulses for superconducting qubit systems with local control theory

    E-CAM Case Study: Designing control pulses for superconducting qubit systems with local control theory

    Dr. Momir Mališ, École Polytechnique Fédérale de Lausanne, Switzerland   Abstract A quantum logic gate is one of the key components of the quantum computer, and designing an effective quantum universal gate is one of the major goals in the development of quantum computers. We have developed a software based …Read More »
  • Spring shooting – A module for improving efficiency of transition path sampling

    Spring shooting – A module for improving efficiency of transition path sampling

      Transition path sampling is most efficient when paths are generated from the top of the free energy barrier. However, complex (biomolecular) activated processes, such as nucleation or protein binding/unbinding, can have asymmetric and peaked barriers. Using uniform selection on these type of processes will not be efficient, as it, …Read More »
  • New publication is out: “Adaptive Resolution Molecular Dynamics Technique: Down to the Essential”

    New publication is out: “Adaptive Resolution Molecular Dynamics Technique: Down to the Essential”

      A new publication by the Theoretical and Mathematical Physics in Molecular Simulation group of the Freie Universität Berlin, lead by Prof. Luigi Delle Site, E-CAM partner, was published in the Journal of Chemical Physics. In it, the authors study the application of the thermodynamic force in the coupling region of an …Read More »
  • Symmetry Adapted Wannier Functions – a Component of the Wannier90

    Symmetry Adapted Wannier Functions – a Component of the Wannier90

      Symmetry Adapted Wannier Functions is a module within Wannier90 which is devoted to the construction of Wannier function (WF) with a given symmetry. The procedure implemented in this module enables one to control the symmetry and center of the WFs and also simplifies the minimisation of the spread functional …Read More »
  • Meet us at the PASC18 conference in Basel on 2-4 July 2018

    Meet us at the PASC18 conference in Basel on 2-4 July 2018

        E-CAM will have an exhibition stand at the PASC18 Conference, that will be held from July 2 to 4, 2018 at the Congress Center Basel, Switzerland. PASC18 PASC18 is the fifth edition of the PASC Conference series, an international platform for the exchange of competences in scientific computing …Read More »
  • PIM_wd: Module for sampling of the quantum Wigner distribution

    PIM_wd: Module for sampling of the quantum Wigner distribution

      The PIM_wd module implements the exact quantum Wigner probability distribution function sampling algorithm of the Phase Integration Method [1], and is the main subroutine for the quantum correlation function calculations in the PaPIM code. The module samples the thermal Wigner density using a generalised Monte Carlo scheme for sampling …Read More »
  • PRACE Workshop on HPC in Molecular and Atomistic Simulations @ICHEC

    PRACE Workshop on HPC in Molecular and Atomistic Simulations @ICHEC

    ICHEC, in a collaboration with E-CAM, is organizing a funded PRACE course at the University College Dublin from 13th to 15th June 2018 for all interested in the use of HPC in their molecular and atomistic simulations. This course aims to provide a general overview of HPC and relevant applications …Read More »
  • HPC-in-a-day Workshop

    HPC-in-a-day Workshop

      A one day hands-on HPC workshop organized by CECAM, E-CAM and ICHEC was held at the University College Dublin on May 29, 2018.Read More »
  • Issue 8 – May 2018

    Issue 8 – May 2018

      E-CAM Newsletter of May 2018   Get the latest news from E-CAM, sign up for our quarterly newsletter.Read More »
  • High Throughput Computing Workshop

    High Throughput Computing Workshop

    E-CAM is organising a one week (16-20 July 2018) Extended Software Development Workshop in Turin, Italy that will focus on intelligent high throughput computing (HTC) as a technique that crosses many domains within the molecular simulation community in general and the E-CAM community in particular. The workshop will be a hybrid learning/coding …Read More »
  • The launch of the E-CAM Online Training Portal

    The launch of the E-CAM Online Training Portal

      We are pleased to announce that our E-CAM training portal is now online. Access instructions here. The goals and expected impacts for our online training infrastructure are to:   Collect the content captured at our Extended Software Development Workshops (ESDWs), allowing participants to re-visit lectures or demonstrations in their …Read More »
  • E-CAM Case Study: The implementation of a hierarchical equilibration strategy for polymer melts, to help studying the rheological properties of new composite materials

    E-CAM Case Study: The implementation of a hierarchical equilibration strategy for polymer melts, to help studying the rheological properties of new composite materials

    Dr. Hideki Kobayashi, Max-Planck-Institut für Polymerforschung, Germany Abstract The ability to accurately determine and predict properties of newly developed polymer materials is highly important to researchers and industry, but at the same time represents a significant theoretical and computational challenge. We have developed a novel multiscale simulation method based on …Read More »
  • Coarse-Graining module, a Component of the Hierarchical Equilibration Strategy for Polymer Melts

    Coarse-Graining module, a Component of the Hierarchical Equilibration Strategy for Polymer Melts

    To study the properties of polymer melts by numerical simulations, equilibrated configurations must be prepared. However, the relaxation time for high molecular weight polymer melts is huge and increases, according to reptation theory, with the third power of the molecular weight. Hence, an effective method for decreasing the equilibration time …Read More »
  • 6 software modules recently delivered in the area of Quantum Dynamics

      In this report for Deliverable 3.3 of E-CAM [1], 6 software modules in quantum dynamics are presented. Four modules stem from some of the activities performed during the Extended Software Development Workshop (ESDW) held by E-CAM at University College Dublin in July 2017 and originate from input of E-CAM’s …Read More »
  • New report published:  Identification / Selection of E-CAM Electronic Structure Codes for Development

    New report published: Identification / Selection of E-CAM Electronic Structure Codes for Development

      Read our latest report on the state of the art codes and methods in Quantum Monte Carlo, Density Functional Theory (DFT) and beyond DFT methods. This report contains a review of the software available in these areas and on the basic features that the majority of these codes have …Read More »
  • Open call for CECAM flagship event proposals 2019

    Open call for CECAM flagship event proposals 2019

        The CECAM CALL for workshops and schools that will run from April 2019 to March 2020 is now open! The text for the call and information on how to submit a proposal can be found at https://www.cecam.org/submitting.html. Deadline for submissions is 16 July 2018.   Good luck!  Read More »
  • Contact Map – a package for analyzing and exploring contacts, from a trajectory generated by MD

    Contact Map – a package for analyzing and exploring contacts, from a trajectory generated by MD

      Contacts can be an important tool for defining (meta)stable states in processes involving biomolecules. For example, an analysis of contacts can be particularly useful when defining bound states during a binding processes between proteins, DNA, and small molecules (such as potential drugs). The contacts analyzed by the contact_map package …Read More »
  • Scientific reports from the 2017 E-CAM workshops, are now available on our website

    Scientific reports from the 2017 E-CAM workshops, are now available on our website

      The scientific reports* from the following workshops conducted in year 2 of the project E-CAM (2017): E-CAM Scoping Workshop: “From the Atom to the Material” , 18- 20 September 2017, University of Cambridge, UK, E-CAM State-of-the-Art Workshop WP4: Meso and Multiscale Modelling, 29 May – 1 June 2017, University …Read More »
  • New report published: Identification / Selection of E-CAM Quantum Dynamics Codes for Development

      As technologies reach atomic length and energy scales, the simulation of quantum effects acquires practical interest beyond basic science in areas ranging from sustainable energy, to medicine, to quantum computing. Brute force simulation of quantum dynamical properties, however, is currently out of reach due to the exponential scaling of …Read More »
  • Metal-ion force field developed by E-CAM using novel Machine Learning procedure is now available for download

    Metal-ion force field developed by E-CAM using novel Machine Learning procedure is now available for download

      The database of the force fields developed by the SNS SMART group (SNS, Pisa, Italy), including the metal-ions force fields optimized within E-CAM using novel Machine Learning procedure (reported in a recent publication[1] and in a case study reported by E-CAM here), are now available for download at http://smart.sns.it/vmd_molecules/. …Read More »
  • LocConQubit, a module for the construction of controlled pulses on isolated qubit systems using the Local Control Theory

    LocConQubit, a module for the construction of controlled pulses on isolated qubit systems using the Local Control Theory

      The LocConQubit module implements the Local Control Theory[1,2], an algorithm for on-the-fly construction of a time-dependent potential that drives the evolution of a Hamiltonian towards one of its eigenstates. The algorithm is applicable to any Hamiltonian that is separable into a time-dependent and into a time-independent part, where the …Read More »
  • E-CAM flyer with 2018 workshop program

    E-CAM flyer with 2018 workshop program

    E-CAM-Flyer18 Download FlyerRead More »
  • Issue 7 – January 2018

    Issue 7 – January 2018

      E-CAM Newsletter of January 2018   Get the latest news from E-CAM, sign up for our quarterly newsletter.Read More »
  • The simulation of metal ions in protein-water systems using machine learning: An E-CAM case study and conversation

    The simulation of metal ions in protein-water systems using machine learning: An E-CAM case study and conversation

      With Dr. Francesco Fracchia, Scuola Normale Superiore di Pisa Interviewer: Dr. Donal Mackernan, University College Dublin   Abstract One quarter to one third of all proteins require metals to function but the description of metal ions in standard force fields is still quite primitive. In this case study and …Read More »
  • GRASP Sampling – a module to build a representative data set for a fitting procedure

    GRASP Sampling – a module to build a representative data set for a fitting procedure

    GRASP_sampling performs a stratified sampling of the configurations, described by vectors, of a system to build a representative training set in a fitting procedure. Given a list of candidate configurations, and selected the size (N) of the training set required, the module executes the combinatorial optimization that maximizes the following …Read More »
  • From Rational Design of Molecular Biosensors to Patent and potential Start-up

    From Rational Design of Molecular Biosensors to Patent and potential Start-up

      Dr. Donal Mackernan, University College Dublin Abstract The power of advanced simulation combined with statistical theory , experimental know-how and high performance computing is used to design a protein based molecular switch sensor with remarkable sensitivity and significant industry potential. The sensor technology has applications across commercial markets including …Read More »
  • New publication using the GC-AdResS molecular dynamics technique

      The publication “Probing spatial locality in ionic liquids with the grand canonical adaptive resolution molecular dynamics technique (GC-AdResS)“ by the Theoretical and Mathematical Physics in Molecular Simulation group of the Freie Universität Berlin, lead by Prof.Luigi Delle Site, E-CAM partner, describes the use of the GC-AdResS molecular dynamics technique …Read More »
  • E-CAM program of events 2018 is out

    E-CAM program of events 2018 is out

    Check out our program of events for this year, running from April 2018 to February 2019: E-CAM Events 2018 See the workshop details to learn how to apply. E-CAM events are part of the annual CECAM flagship program, and are hosted at the different CECAM Nodes locations. E-CAM runs three …Read More »
  • New article is out: “Force Field Parametrization of Metal Ions from Statistical Learning Techniques”

      This paper from E-CAM partners working in Scuola Normale Superiore (Pisa, Italy) describes a novel statistical procedure, developed to optimize the parameters of non-bonded force fields of metal ions in soft matter. The paper is open access and can be downloaded directly from ACS’s page at http://pubs.acs.org/doi/10.1021/acs.jctc.7b00779. This work …Read More »
  • Geomoltools: A set of software modules to easily manipulate molecular geometries

    Geomoltools is a set of eight pre- and post-treatment Fortran codes that can be used to easily manipulate molecular geometries, allowing to minimize the average energy obtained for a range of internuclear distances for the dimers of each element, and decrease the computational cost of a DFT calculation. The set …Read More »
  • Issue 6 – October 2017

    Issue 6 – October 2017

      E-CAM Newsletter of October 2017Read More »
  • Path density for OpenPathSampling

    Module path density implements path density calculations for the OpenPathSampling (OPS) package, including a generic multidimensional sparse histogram, and plotting functions for the two-dimensional case. Path density plots provide a way to visualize kinetic information obtained from path sampling, such as the mechanism of a rare event. In addition, the …Read More »
  • Second-Order Differencing Scheme

    This module, SodLib, provides exact wavefunction propagation using the second-order differencing (SOD) integrator scheme to solve the time-dependent Schrödinger equation as described by Leforestier et al, J. Comp Phys, 94, 59-80, 1991. Within this scheme the time interval is determined through dividing hbar by the eigenvalue of the Hamiltonian operator …Read More »
  • A Conversation on Neural Networks, from Polymorph Recognition to Acceleration of Quantum Simulations

    A Conversation on Neural Networks, from Polymorph Recognition to Acceleration of Quantum Simulations

      With Prof. Christoph Dellago (CD), University of Vienna, and Dr. Donal Mackernan (DM), University College Dublin.   Abstract Recently there has been a dramatic increase in the use of machine learning in physics and chemistry, including its use to accelerate simulations of systems at an ab-initio level of accuracy, …Read More »
  • First GPU version of the DL_MESO_DPD code

    DL_MESO_DPD, is the Dissipative Particle Dynamics (DPD) code from the mesoscopic simulation package DL_MESO [1], developed by Dr. Michael Seaton at Daresbury Laboratory (UK). This open source code is available from Science and Technology Facilities Council (STFC) under both academic (free) and commercial (paid) licenses. E-CAM’s Work-package 4 (WP4), Meso …Read More »
  • New E-CAM modules based on DL_MESO_DPD

    New E-CAM modules based on DL_MESO_DPD

      The software DL_MESO_DPD, is the Dissipative Particle Dynamics (DPD) code from the mesoscopic simulation package DL_MESO[1], developed by Dr. Michael Seaton at Daresbury Laboratory (UK). This open source code is available from Science and Technology Facilities Council (STFC) under both academic (free) and commercial (paid) licenses.Read More »
  • Rare events, path sampling and the OpenPathSampling package

    Rare events, path sampling and the OpenPathSampling package

      In the last few years, modelling of rare events has made tremendous progress and several computational methods have been put forward to study these events. Despite this effort, new approaches have not yet been included, with adequate efficiency and scalability, in common simulation packages. One objective of the Classical …Read More »
  • LibOMM : Orbital Minimization Method Library

    Purpose The library LibOMM solves the Kohn-Sham equation as a generalized eigenvalue problem for a fixed Hamiltonian. It implements the orbital minimization method (OMM), which works within a density matrix formalism. The basic strategy of the OMM is to find the set of Wannier functions (WFs) describing the occupied subspace …Read More »
  • AI Quantum Breakthrough: ANAKIN-ME Webinar

    AI Quantum Breakthrough: ANAKIN-ME Webinar

    The development of a new methodology, known as Accurate NeurAl networK engINe for Molecular Energies (ANAKIN-ME, or ANI for short), is able, it is claimed,  to describe the forces in molecules as accurately as density functional theory (DFT), but hundreds of thousands of times faster. This combination of speed and accuracy …Read More »
  • Webinars series: Best Practices for HPC Software Developers

    E-CAM strongly recommends software developers interested in HPC to attend the webinar series on Best Practices for HPC organized by the IDEAS project in collaboration with the DOE/ASCR computing facilities (ALCF, NERSC, and OLCF), and the Exascale Computing Project (ECP). Information on the webinars programme available here.Read More »
  • Analysis of charge dipole moments in DL_MESO_DPD

    The present module, gen_dipole.f90, is a generalization of the dipole.f90 post-processing utility of DL_MESO_DPD, the Dissipative Particle Dynamics (DPD) code from the DL_MESO package. It processes the trajectory (HISTORY) files to obtain the charge dipole moments of all the (neutral) molecules in the system. It produces files dipole_* containing the …Read More »
  • Solvers for quantum atomic radial equations

    SQARE (solvers for quantum atomic radial equations) is a library of utilities intended for dealing with functions discretized on radial meshes, wave-equations with spherical symmetry and their corresponding quantum states. The utilities are segregated into three levels: radial grids and functions, ODE solvers, and states. For more information see modules …Read More »
  • E-CAM in the organizing committee of CECAM workshop on Quantum Computing and HPC

    E-CAM in the organizing committee of CECAM workshop on Quantum Computing and HPC

    An event to bring together the quantum information and HPC communities to discuss their specific expertise and outline the bridges that will eventually identify: (1) the future role of quantum technologies in scientific fields where HPC is currently dominant; (2) the use of existing HPC platforms to demonstrate the potentialities …Read More »
  • Workshop for Industrial EsD users @ ISC17

    Workshop for Industrial EsD users @ ISC17

    The ETP4HPC initiative is inviting the industrial HPC users to a attend a workshop in June 22, Frankfurt, to discuss their needs and expectations regarding the potential use of Extreme Scale Demonstrators’ (EsDs). For more information on the workshop please visit the workshop webpage: http://www.etp4hpc.eu/en/industrial-use-of-esds-isc17.html  Read More »
  • E-CAM has a new front page

    E-CAM has a new front page

    Take a look at our new front page: check out our upcoming events; latest news; stories; learn more about some of our software developments; among many others interesting topics. We look forward to your visit!Read More »
  • ClassMC

    Module ClassMC samples the system phase space using the classical Boltzmann distribution function and calculates the time correlation functions from the sampled initial conditions. For more information check the module documentation here.Read More »
  • Direct MD (on-the-fly) flux/rate in OpenPathSampling

    This module, based on OpenPathSampling, calculates the flux out of a state and through an interface, or the rate of the transition between two states, while running a trajectory. For more information check the module documentation here.  Read More »
  • Does our simulation community need EXASCALE ?

    By Prof. David Ceperley, University of Illinois Urbana-Champaign The computer simulation of electrons, atoms, molecules, and their assemblies in soft and hard matter is foundational for many scientific disciplines and important commercially. Exascale computing is coming and our community should take part as are our colleagues in lattice gauge theory, …Read More »
  • Technology transfer from the academic world to industry is a difficult process in all scientific fields

    By Prof. Mike Payne, University of Cambridge In many countries there is increasing demand for measurable socio-economic impact from academic research. Perhaps the UK is furthest down this path with a significant fraction of the funding for Universities dependent on the ‘Impact’ (defined as impact outside of academia) of the …Read More »
  • High Performance Computing, Computer Simulation, and Theoretical Physics: Evolution or Revolution?

    By Prof. Giovanni Ciccotti, University of Rome La Sapienza Numerical physics, i.e. numerical calculations serving the needs of traditional theoretical physics, exists at least since the times of Galileo, and probably long before. As Computer Simulation (started with solving problems in Statistical Mechanics), it exists only since the end of …Read More »
  • New newsletter is out

    New newsletter is out

    In our fifth newsletter, we highlight the programme of events 2017, and present the profiles of the new Project Technical Manager, Ignacio Pagonabarraga, and the Project Coordinator, Ana Catarina Mendonça. We describe the nature of the E-CAM extended software development workshops and the outputs from these events in 2016, and …Read More »
  • E-CAM article on the Psi-k Newsletter

    E-CAM article on the Psi-k Newsletter

    The Psi-k Newsletter of December 2016 presents articles on the European Centers of Excellence NOMAD, E-CAM and MaX, highlighting what they are developing and can offer to the community. View article here.Read More »
  • Issue 5 – January 2017

    Issue 5 – January 2017

    In our fifth newsletter, we highlight the programme of events 2017, and present the profiles of the new Project Technical Manager, Ignacio Pagonabarraga, and the Project Coordinator, Ana Catarina Mendonça. We describe the nature of the E-CAM extended software development workshops and the outputs from these events in 2016, and …Read More »
  • Issue 4 – September 2016

    Issue 4 – September 2016

    In our fourth newsletter read about the outcomes of some of our first workshops. Download NewsletterRead More »
  • Issue 3 – June 2016

    Issue 3 – June 2016

    In our third edition of the E-CAM quarterly find the full programme of our training events for the rest of 2016 as well as profiles of all of our postdocs and programmers. The Editorial, by Prof Mike Payne, is a wonderful discussion on technology transfer between academia and industry. Download NewsletterRead More »
  • Issue 2 – March 2016

    Issue 2 – March 2016

    In our second edition of the E-CAM Quarterly find the full list of all of our training events and employment opportunities. The Editorial features Professor Giovanni Ciccotti who asks whether all of the HPC advances are an evolution or a revolution. Download NewsletterRead More »
  • Issue 1 – January 2016

    Issue 1 – January 2016

    Abstract Issue 1 – January 2016 The first E-CAM newsletter highlighting our kick-off meeting in Dublin in October 2015, our first management team appointments, and the E-CAM “Science View”. Download NewsletterRead More »

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