scholarly journals NAMD - The Engine for Large-Scale Classical MD Simulations of Biomolecular Systems Based on a Polarizable Force Field: ALCF-2 Early Science Program Technical Report

2013 ◽  
Author(s):  
B. Roux ◽  
Y. Luo ◽  
W. Jiang
Keyword(s):  
Force Field ◽  
Large Scale ◽  
Md Simulations ◽  
Science Program ◽  
Biomolecular Systems ◽  
Polarizable Force Field ◽  
Technical Report

scholarly journals Wrapping up Viruses at Multiscale Resolution: Optimizing PACKMOL and SIRAH Execution for Simulating the Zika Virus.

2020 ◽  
Author(s):  
Martín Soñora ◽  
Leandro Martinez ◽  
Sergio Pantano ◽  
Matías R. Machado
Keyword(s):  
Force Field ◽  
Zika Virus ◽  
Packing Problem ◽  
Md Simulations ◽  
Coarse Grained ◽  
Test Case ◽  
Biomolecular Systems ◽  
Enveloped Virus ◽  
Anionic Phospholipids ◽  
Detailed Structural Analysis

<p> Simulating huge biomolecular complexes of million atoms at relevant biological timescales is becoming accessible to the broad scientific community. That proves to be crucial for urgent responses against emergent diseases in real time. Yet, there are still issues to sort regarding the system setup so that Molecular Dynamics (MD) simulations can be run in a simple and standard way. Here, we introduce an optimized pipeline for building and simulating enveloped virus-like particles (VLP). First, the membrane packing problem is tackled with new features and optimized options in PACKMOL. This allows preparing accurate membrane models of thousands of lipids in the context of a VLP within a few hours using a single CPU. Then, the assembly of the VLP system is done within the multiscale framework of the coarse-grained SIRAH force field. Finally, the equilibration protocol provides a system ready for production MD simulations within a few days on broadly accessible GPU resources. The pipeline is applied to study the Zika Virus as a test case for large biomolecular systems. The VLP stabilizes at approximately 0.5 microseconds of MD simulation, reproducing correlations greater than 0.90 against experimental density maps from cryo-electron microscopy. Detailed structural analysis of the protein envelope also shows very good agreement in root mean square deviations and B-factors with the experimental data. The level of details attained shows for the first time a possible role of anionic phospholipids in stabilizing the envelope. Combining an efficient and reliable setup procedure with an accurate coarse-grained force field provides a valuable pipeline for simulating arbitrary viral systems or sub-cellular compartments, paving the way towards whole-cell simulations.</p>

scholarly journals Extreme Scalability of DFT-Based QM/MM MD Simulations Using MiMiC

2019 ◽  
Author(s):  
Viacheslav Bolnykh ◽  
Jógvan Magnus Haugaard Olsen ◽  
Simone Meloni ◽  
Martin P. Bircher ◽  
Emiliano Ippoliti ◽  
...  
Keyword(s):  
Large Scale ◽  
Md Simulations ◽  
Coupling Scheme ◽  
Loose Coupling ◽  
Tight Coupling ◽  
Modeling Framework ◽  
Biomolecular Systems ◽  
Computational Overhead ◽  
Coupling Strategy ◽  
High Flexibility

We present a highly scalable DFT-based QM/MM implementation developed within MiMiC, a recently introduced multiscale modeling framework that uses a loose-coupling strategy in conjunction with a multiple-program multiple-data (MPMD) approach. The computation of electrostatic QM/MM interactions is parallelized exploiting both distributed- and shared-memory strategies. Here, we use the efficient CPMD and GROMACS programs as QM and MM engines, respectively. The scalability is demonstrated through large-scale benchmark simulations of realistic biomolecular systems employing GGA and hybrid exchange-correlation functionals. We show that the loose-coupling strategy adopted in MiMiC, with its inherent high flexibility, does not carry any significant computational overhead compared to a tight-coupling scheme. Furthermore, we demonstrate that the adopted parallelization strategy enables scaling of up to 13,000 CPU cores with efficiency above 70%, thus making DFT-based QM/MM MD simulations using hybrid functionals at the nanosecond scale accessible.

scholarly journals Wrapping up Viruses at Multiscale Resolution: Optimizing PACKMOL and SIRAH Execution for Simulating the Zika Virus.

2020 ◽  
Author(s):  
Martín Soñora ◽  
Leandro Martinez ◽  
Sergio Pantano ◽  
Matías R. Machado
Keyword(s):  
Force Field ◽  
Zika Virus ◽  
Packing Problem ◽  
Md Simulations ◽  
Coarse Grained ◽  
Test Case ◽  
Biomolecular Systems ◽  
Enveloped Virus ◽  
Anionic Phospholipids ◽  
Detailed Structural Analysis

<p> Simulating huge biomolecular complexes of million atoms at relevant biological timescales is becoming accessible to the broad scientific community. That proves to be crucial for urgent responses against emergent diseases in real time. Yet, there are still issues to sort regarding the system setup so that Molecular Dynamics (MD) simulations can be run in a simple and standard way. Here, we introduce an optimized pipeline for building and simulating enveloped virus-like particles (VLP). First, the membrane packing problem is tackled with new features and optimized options in PACKMOL. This allows preparing accurate membrane models of thousands of lipids in the context of a VLP within a few hours using a single CPU. Then, the assembly of the VLP system is done within the multiscale framework of the coarse-grained SIRAH force field. Finally, the equilibration protocol provides a system ready for production MD simulations within a few days on broadly accessible GPU resources. The pipeline is applied to study the Zika Virus as a test case for large biomolecular systems. The VLP stabilizes at approximately 0.5 microseconds of MD simulation, reproducing correlations greater than 0.90 against experimental density maps from cryo-electron microscopy. Detailed structural analysis of the protein envelope also shows very good agreement in root mean square deviations and B-factors with the experimental data. The level of details attained shows for the first time a possible role of anionic phospholipids in stabilizing the envelope. Combining an efficient and reliable setup procedure with an accurate coarse-grained force field provides a valuable pipeline for simulating arbitrary viral systems or sub-cellular compartments, paving the way towards whole-cell simulations.</p>

scholarly journals Extreme Scalability of DFT-Based QM/MM MD Simulations Using MiMiC

2019 ◽  
Author(s):  
Viacheslav Bolnykh ◽  
Jógvan Magnus Haugaard Olsen ◽  
Simone Meloni ◽  
Martin P. Bircher ◽  
Emiliano Ippoliti ◽  
...  
Keyword(s):  
Large Scale ◽  
Md Simulations ◽  
Coupling Scheme ◽  
Loose Coupling ◽  
Tight Coupling ◽  
Modeling Framework ◽  
Biomolecular Systems ◽  
Computational Overhead ◽  
Coupling Strategy ◽  
High Flexibility

We present a highly scalable DFT-based QM/MM implementation developed within MiMiC, a recently introduced multiscale modeling framework that uses a loose-coupling strategy in conjunction with a multiple-program multiple-data (MPMD) approach. The computation of electrostatic QM/MM interactions is parallelized exploiting both distributed- and shared-memory strategies. Here, we use the efficient CPMD and GROMACS programs as QM and MM engines, respectively. The scalability is demonstrated through large-scale benchmark simulations of realistic biomolecular systems employing GGA and hybrid exchange-correlation functionals. We show that the loose-coupling strategy adopted in MiMiC, with its inherent high flexibility, does not carry any significant computational overhead compared to a tight-coupling scheme. Furthermore, we demonstrate that the adopted parallelization strategy enables scaling of up to 13,000 CPU cores with efficiency above 70%, thus making DFT-based QM/MM MD simulations using hybrid functionals at the nanosecond scale accessible.

Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model

1999 ◽  
Vol 110 (2) ◽  
pp. 741-754 ◽  
Author(s):  
Jay L. Banks ◽  
George A. Kaminski ◽  
Ruhong Zhou ◽  
Daniel T. Mainz ◽  
B. J. Berne ◽  
...  
Keyword(s):  
Force Field ◽  
Ab Initio ◽  
Point Charge ◽  
Point Charge Model ◽  
Polarizable Force Field ◽  
Charge Model

Molecular Dynamics Study of Hydration in Ethanol−Water Mixtures Using a Polarizable Force Field†

2005 ◽  
Vol 109 (14) ◽  
pp. 6705-6713 ◽  
Author(s):  
Sergei Yu. Noskov ◽  
Guillaume Lamoureux ◽  
Benoît Roux
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Polarizable Force Field
Sign in / Sign up

Export Citation Format

Share Document