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By Stefan Doerr Molecular dynamics has matured to the point where users can simulate multiple protein systems over timescales as large as milliseconds (see reference of HTMD and ACEMD at https://www.acellera.com/science/). However, the preparation of the protein systems remains a complex step. Tools already exist which allow the preparation of an MD system using visual

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By Gerard Martínez-Rosell PlayMolecule Introduction One step of the simulation workflow has typically remained relatively underdressed, namely, the preparation steps before building a molecular system. These preparation steps aim to make a protein structure, usually extracted from the PDB database, ready for system building. In particular, there’s two main points that need to be addressed:

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From Stefan Doerr Introduction Proteins are essential in the regulation of most of the processes in a cell. They do so by interacting with other molecules, including other proteins. Protein-protein interactions have been the subject of study for a long time using both experimental and computational methods, however they have eluded the atomic-level analysis and

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By Gerard Martinez-Rosell Introduction ACEMD was introduced in the field of Molecular Dynamics (MD) back in 2008. Its release, together with other MD engines, revolutionized the simulation throughput by leveraging the intrinsic parallelism present in a specific computer processor termed GPU (Graphic Processor Unit). Using a cluster of GPUs or a distributed network like GPUGRID

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By Alex Perálvarez-Marín Introduction: In Wang et al. we have studied and described an intermediate step of the molecular mechanism of sugar transport thanks to the possibility to run several MD simulation replicates in the 100 ns range using a single GPU-based desktop running ACEMD. Our solvated membrane protein system embedded in the lipid bilayer

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