gpu version of the pmemd engine (Molecular Dynamics Inc)

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Molecular Dynamics Inc gpu version of the pmemd engine
Gpu Version Of The Pmemd Engine, supplied by Molecular Dynamics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/pmemd+engine/gpu+code+pmemd/pmc07256942-267-11-0
Average 90 stars, based on 1 article reviews

gpu version of the pmemd engine - by Bioz Stars, 2026-10

90/100 stars

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Article Title: Pharmacophore-based virtual screening for identifying β5 subunit inhibitor of 20S proteasome.
Article Snippet: Proteasomal system plays an important role in maintaining cell homeostatis.. Overexpression of proteasomes leads to several major diseases, such as cancer and autoimmune disorder.. The β5 subunit of proteasome is a crucial active site in proteolysis, and targeting proteasome β5 subunit is essential for proteasome inhibition.

Article Title: Role of Structural Dynamics in Selectivity and Mechanism of Non-heme Fe(II) and 2-Oxoglutarate-Dependent Oxygenases Involved in DNA Repair
Article Snippet: Molecular dynamics simulations were performed using the GPU version of the PMEMD engine integrated with Amber16.

Article Title: Inverted Binding of Non-natural Substrates in Strictosidine Synthase Leads to a Switch of Stereochemical Outcome in Enzyme-Catalyzed Pictet–Spengler Reactions
Article Snippet: Molecular Dynamics Simulations: Simulations were performed using the GPU code (pmemd)17 of the Amber 12 package.18 Parameters for the carbocationic intermediate substrates were generated within the antechamber module using the general AMBER force field (gaff)19, with partial charges set to fit the electrostatic potential generated at the HF/6‐31G(d) level by the RESP model.20 The charges were calculated according to the Merz‐Singh‐Kollman scheme 21 using Gaussian 09.

Article Title: A Biocatalytic Platform for Synthesis of Chiral α- Trifluoromethylated Organoborons
Article Snippet: Molecular Dynamics simulations were performed using the GPU code (pmemd) [39] of the AMBER 16 package [40].

Article Title: Critical role of inter-domain interactions on the conformational change and catalytic mechanism of Endoplasmic Reticulum Aminopeptidase 1
Article Snippet: Conventional Molecular Dynamics Simulations Conventional (cMD) and accelerated (aMD) molecular dynamics simulations were performed with the GPU-version of PMEMD program using periodic boundary conditions 24 .

Software:

Article Title: Key allosteric and active site residues of SARS-CoV-2 3CLpro are promising drug targets
Article Snippet: .. Molecular dynamics (MD) simulations were performed using the PMEMD engine within the Amber 20 software suite [93,94,101]. ..

Variant Assay:

Article Title: Oleanolic acid purified from the stem bark of Olax subscorpioidea Oliv. inhibits the function and catalysis of human 17 β -hydroxysteroid dehydrogenase 1.
Article Snippet: Docking scores (highest negative energy in kcal/mol) were determined, and docked poses were visualised using BIOVIA Discovery Studio Visualizer 2021 client (Adewumi et al., 2023). .. Molecular dynamics (MD) simulation was performed using the GPU version of the PMEMD.CUDA engine (Lee et al., 2017) provided with the AMBER package, FF18SB variant of the AMBER forcefield used to describe the protein (Case et al., 2018). ..

Generated:

Article Title: Role of mutations in a chemoenzymatic enantiodivergent C(sp 3 )–H insertion: exploring the mechanism and origin of stereoselectivity
Article Snippet: .. Molecular Dynamics simulations were performed using the GPU code (pmemd) of the Amber18 package.22 Parameters for the heme unit were generated within the antechamber and MCPB.py23 modules in the Amber18 package and the general AMBER forcefield (gaff)24 with partial charges set to fit the electrostatic potential generated at the B3LYP/6-31G** level by the RESP model.25 The charges were calculated according to the Merz–Singh–Kollman scheme26,27 using the Gaussian 16 package. ..

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