Abrupt GC-AdResS: A new and more general implementation of the Grand Canonical Adaptive Resolution Scheme (GC-AdResS)

The Grand Canonical Adaptive resolution scheme (GC-AdResS) gives a methodological description to partition a simulation box into different regions with different degrees of accuracy. For more details on the theory see Refs. [1,2,3].

In the context of an E-CAM pilot project focused on the development of the GC-AdResS scheme, an updated version of GC-AdResS was built and implemented in GROMACS, as reported in https://aip.scitation.org/doi/10.1063/1.5031206 (open access version: https://arxiv.org/abs/1806.09870). The main goal of the project is to develop a library or recipe with which GC-AdResS can be implemented in any Classical MD Code.

The current implementation of GC- AdResS in GROMACS has several performance problems. We know that the main performance loss of AdResS simulations in GROMACS is in the neighbouring list search and the generic serial force kernel, linking the atomistic (AT) and coarse grained (CG) forces together via a smooth weighting function. Thus, to get rid of the bottleneck with respect to performance and a hindrance regarding the easy/general implementation into other codes and thus get rid of the not optimized force kernel used in GROMACS we had to change the neighbourlist search. This lead to a considerable speed up of the code. Furthermore it decouples the method directly from the core of any MD code, which does not hinder the performance and makes the scheme hardware independent[4].

This module presents a very straight forward way to implement a new partitioning scheme in GROMACS . And this solves two problems which affect the performance, the neighborlist search and the generic force kernel.

Information about module purpose, background information, software installation, testing and a link to the source code, can be found in our E-CAM software Library here.

E-CAM Deliverables D4.3[5] and D4.4[6] present more modules developed in the context of this pilot project.

References

[1] L. Delle Site and M. Praprotnik, “Molecular Systems with Open Boundaries: Theory and Simulation,” Phys. Rep., vol. 693, pp. 1–56, 2017

[2] H.Wang, C. Schütte, and L.Delle Site, “Adaptive Resolution Simulation (AdResS): A Smooth Thermodynamic and Structural Transition fromAtomistic to Coarse Grained Resolution and Vice Versa in a Grand Canonical Fashion,” J. Chem. Theory Comput., vol. 8, pp. 2878–2887, 2012

[3] H. Wang, C. Hartmann, C. Schütte, and L. Delle Site, “Grand-Canonical-Like Molecular-Dynamics Simulations by Using an Adaptive-Resolution Technique,” Phys. Rev. X, vol. 3, p. 011018, 2013

[4] C. Krekeler, A. Agarwal, C. Junghans, M. Prapotnik and L. Delle Site, “Adaptive resolution molecular dynamics technique: Down to the essential”, J. Chem. Phys. 149, 024104

[5] B. Duenweg, J. Castagna, S. Chiacchera, H. Kobayashi, and C. Krekeler, “D4.3: Meso– and multi–scale modelling E-CAM modules II”, March 2018 . [Online]. Available: https://doi.org/10.5281/zenodo.1210075

[6] B. Duenweg, J. Castagna, S. Chiacchera, and C. Krekeler, “D4.4: Meso– and multi–scale modelling E-CAM modules III”, Jan 2019 . [Online]. Available: https://doi.org/10.5281/zenodo.2555012

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E-CAM related work labeled as “Excellent Science” by the EC Innovation Radar Initiative

The Innovation Radar aims to identify high-potential innovations and innovators. It is an important source of actionable intelligence on innovations emerging from research and innovation projects funded through European Union programmes.

E-CAM is associated to the following Innovations (Innovation topic: excellence science):

    1. Improved Simulation Software Packages for Molecular Dynamics (see link)
    2. Improved software modules for Meso– and multi–scale modelling (see link)

Related to the work of our E-CAM funded Postdoctoral researchers supervised by scientists in the team, working on:

  • Development of the OpenPathSampling package to study rare events  (Universiteit van Amsterdam). Link1
  • Implementation of GPU version of DL_MESO_DPD (Hartree Centre (STFC)). Link
  • Development of polarizable mesoscale model for DL_MESO_DPD (Hartree Centre (STFC)). Link
  • Development of the GC-AdResS scheme (Freie Universitaet Berlin). Link

  • Implementation of hierarchical strategy on ESPResSO++ (Max Plank Institute for Polymer Research, Mainz). Link
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New E-CAM publication is out: “Molecular Dynamics of Open Systems: Construction of a Mean‐Field Particle Reservoir”



New publication from E-CAM partners working at the Institute of Mathematics of the Freie Universität Berlin:

Molecular Dynamics of Open Systems: Construction of a Mean‐Field Particle Reservoir

Authors: Luigi Delle Site, Christian Krekeler, John Whittaker, Animesh Agarwal, Rupert Klein, and Felix Höfling

Adv. Theory Simul. 2019, 1900014, DOI: 10.1002/adts.201900014 (Open access)

Synopsis

A procedure for the construction of a particle and energy reservoir for the simulation of open molecular systems is presented. The reservoir is made of non‐interacting particles (tracers), embedded in a mean‐field. The tracer molecules acquire atomistic resolution upon entering the atomistic region, while atomistic molecules become tracers after crossing the atomistic boundary.

Abstract

The simulation of open molecular systems requires explicit or implicit reservoirs of energy and particles. Whereas full atomistic resolution is desired in the region of interest, there is some freedom in the implementation of the reservoirs. Here, a combined, explicit reservoir is constructed by interfacing the atomistic region with regions of point-like, non-interacting particles (tracers) embedded in a thermodynamic mean field. The tracer molecules acquire atomistic resolution upon entering the atomistic region and equilibrate with this environment, while atomistic molecules become tracers governed by an effective mean-field potential after crossing the atomistic boundary. The approach is extensively tested on thermodynamic, structural, and dynamic properties of liquid water. Conceptual and numerical advantages of the procedure as well as new perspectives are highlighted and discussed.

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Open Postdoctoral Position in Mesoscale Modeling in Nanostructured Materials


In the context of the EU H2020 project E-CAM we are seeking a highly qualified post-doctoral researcher for an exciting collaborative project on the fundamental challenges of  driven transport in complex media. 

Increasingly, modern technology is addressing problems where fluid transport takes place in submicron sized channels, or in pores. The physical laws of transport in such channels are qualitatively different from those that determine bulk flow; they are poorly understood and, importantly, barely exploited. 

The postdoctoral position will  address complementary aspects related to the fundamental challenges of thermodynamic driving on systems of potential industrial interest. In this respect, the  project will be developed in close contact with an industrial partner. 

The project will involve both algorithmic and scientific developments. The candidate will benefit from existing in-house expertise in lattice Boltzmann methods for non-equilibrium soft materials and will contribute to its extension and use on complex materials out of equilibrium. The project will go  beyond the state-of-the-art macroscopic descriptions of phoresis to capture the effects of solute and surface specificity, solute flexibility, surface wettability and heterogeneity, fluctuations and correlations.

We seek motivated researchers, with theoretical and computational expertise. Candidates should have a background in computer simulation, statistical mechanics, biophysics and/or soft condensed matter.

The project will be carried out at the University of Barcelona, under the supervision of Prof. Ignacio Pagonabarraga, for an initial period of 20 months. Candidates with an appropriate background, who are interested in a cutting-edge research at the interface between physics and the biological sciences, are invited to apply.

We look forward to receiving a CV and 1 referee letter. You can address these  documents, or any additional information you require, to Prof. I. Pagonabarraga by email ipagonabarraga@ub.edu. Review of applications will continue until the position is filled.

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Issue 10 – March 2019

E-CAM Newsletter of March 2019

Get the latest news from E-CAM, sign up for our quarterly newsletter.

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Scientific Report from State-of-the-Art Workshop “Improving the accuracy of ab-initio predictions for materials” is available on our website

The workshop scientific report from the E-CAM State-of-the-Art Workshop Improving the accuracy of ab-initio predictions for materials, that took place on the 17-20 September 2018 at the CECAM-FR-MOSER Node (France), is now available for consultation and download on our website under this link.

Short Description:

The State-of-the-Art workshop in the E-CAM Electronic Structure Work-Package (WP2) gathered together 38 participants from the academic research world, shared in a rather equilibrated fashion among Density Functional Theory, Quantum Monte Carlo and Machine Learning communities, and one industrial researcher from Scienomics. Key topics to the development of the field of computational materials science from first principles were thoroughly discussed, from which the following outcomes have emerged:  (1) Importance of computational benchmarks to assess the accuracy of different methods and to feed the machine learning and neural network schemes with reliable data; (2) Need of a common database, and need to develop a common language across different codes and different computational approaches; (3) Interesting capabilities for neural network methods to develop new correlated wave functions; (4) Cross-fertilizing combination of computational schemes in a multi-scale environment; and (5) Recent progress in Quantum Monte Carlo to further improve the accuracy of the calculations by taking alternative routes. Limitations in the field and open questions were also debated, as described in the workshop scientific report.

Other scientific reports from State of the Art and Scoping workshops can be found at  https://www.e-cam2020.eu/scientific-reports/.

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Scientific Report from State-of-the-Art Workshop “Large Scale activated event simulations” is available on our website

The workshop scientific report from the E-CAM State-of-the-Art Workshop Large scale activated event simulations that took place on the 1-3 October 2018 in the CECAM-AT Node (Austria), is now available for consultation and download on our website under this link.

Short Description:

The State-of-the-Art workshop in the E-CAM classical molecular simulation work-package (WP1)  brought together 40 participants including scientists from non-academic research centres, to discuss computational approaches capable of addressing time scale problems in complex systems in materials science and biophysics. Scientific discussions at the workshop centred around three fundamental computational challenges closely related to the time scale problem of classical MD simulation: (1)  The calculation of the populations of metastable states of an equilibrium system; (2) The sampling of transition pathways between long-lived (meta)stable states and the calculation of reaction rate constants; and (3) The extraction of useful mechanistic information from the simulation data and the construction of low-dimensional models that capture the essential features of the process under study. The main outcomes from each discussion are described in the workshop report.

Two open discussion sessions revolved on efficient path sampling methods and the identification of reaction coordinates; and how machine learning approaches can be used to make progress in this area. Another important goal of the workshop was to debate about how to facilitate the use of simulation and modelling in industrial settings, with the workshop participants with industrial experience emphasing the importance of detailed project management and, in particular, the need to have very clear agreements about intellectual property rights.

Other scientific reports from State of the Art and Scoping workshops can be hound here:  https://www.e-cam2020.eu/scientific-reports/.

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Porting of electrostatics to the GPU version of DL_MESO_DPD


The porting of DL_MESO_DPD [1,2] to graphic cards (GPUs) was reported in deliverable D4.2 of E-CAM[3] (for a single GPU) and deliverable D4.3 [4] (for multiple GPUs) (Figure 1), and has now been extended to include electrostatics, with two alternative schemes as explained below. This work was recently reported on deliverable D4.4[5].

Figure 1: DL_MESO strong scaling results on PizDaint, obtained using 1.8 billion particles for 256 to 2048 GPUs. Results show very good scaling, with efficiency always above 89% for 2048 GPUs.


To allow Dissipative Particle Dynamics (DPD) methods to treat systems with electrically charged particles, several approaches have been proposed in the literature, mostly based on the Ewald summation method [6]. The DL_MESO_DPD  code includes Standard Ewald and Smooth Particle Mesh Ewald (SPME) methods (in version 2.7, released in December 2018). Accordingly, here the same methods are implemented for the single-GPU version of the code. Continue reading…

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Topics in Classical MD – Extended Software Development Workshop

E-CAM is organising an Extended Software Development Workshop in Topics in Classical MD from 3 to 12 April 2019, which is a major coding initiative that will combine lectures; coding sessions and hands-on training.

Topics at this workshop will include using and extending modern MD software in the domains of:

  • advanced path sampling methods (and the software package OpenPathSampling)
  • metadynamics and the calculation of collective variables (and the software package PLUMED)
  • machine learning for molecular dynamics simulatons (including local structure recognition and representation of potential energy surfaces).

In addition, this workshop will feature an emphasis on performance testing and benchmarking software, with particular focus on high performance computing.

This is a great opportunity to bring your software development project in all specialist domains of Classical MD and spend two weeks in the beautiful city of Lyon with other peers and with experienced coders. More information and apply through the CECAM website at: https://www.cecam.org/workshop-1802.html.

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Two papers introducing OpenPathSampling, a software package to study rare events

Two papers introducing to OpenPathSampling (OPS) were recently published : 

Continue reading…

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