Literature DB >> 31999456

Split the Charge Difference in Two! A Rule of Thumb for Adding Proper Amounts of Ions in MD Simulations.

Matías R Machado1, Sergio Pantano1.   

Abstract

Despite the relevance of properly setting ionic concentrations in Molecular Dynamics (MD) simulations, methods or practical rules to set ionic strength are scarce and rarely documented. Based on a recently proposed thermodynamics method we provide an accurate rule of thumb to define the electrolytic content in simulation boxes. Extending the use of good practices in setting up MD systems is promptly needed to ensure reproducibility and consistency in molecular simulations.

Year:  2020        PMID: 31999456     DOI: 10.1021/acs.jctc.9b00953

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  9 in total

1.  Molecular Modeling of ABHD5 Structure and Ligand Recognition.

Authors:  Rezvan Shahoei; Susheel Pangeni; Matthew A Sanders; Huamei Zhang; Ljiljana Mladenovic-Lucas; William R Roush; Geoff Halvorsen; Christopher V Kelly; James G Granneman; Yu-Ming M Huang
Journal:  Front Mol Biosci       Date:  2022-06-28

2.  Withasomniferol C, a new potential SARS-CoV-2 main protease inhibitor from the Withania somnifera plant proposed by in silico approaches.

Authors:  Shivananada Kandagalla; Hrvoje Rimac; Krishnamoorthy Gurushankar; Jurica Novak; Maria Grishina; Vladimir Potemkin
Journal:  PeerJ       Date:  2022-06-02       Impact factor: 3.061

3.  Computational Investigation of Structural Dynamics of SARS-CoV-2 Methyltransferase-Stimulatory Factor Heterodimer nsp16/nsp10 Bound to the Cofactor SAM.

Authors:  Md Fulbabu Sk; Nisha Amarnath Jonniya; Rajarshi Roy; Sayan Poddar; Parimal Kar
Journal:  Front Mol Biosci       Date:  2020-11-24

4.  DFT calculations to investigate silver ions as a virucide from SARS-CoV-2.

Authors:  Jocelia Silva Machado Rodrigues; Aldimar Machado Rodrigues; Divanizia do Nascimento Souza; Erico Raimundo Pereira de Novais; Alzeir Machado Rodrigues; Glaura Caroena Azevedo de Oliveira; Andrea de Lima Ferreira Novais
Journal:  J Mol Model       Date:  2021-10-13       Impact factor: 1.810

5.  A Boron Delivery Antibody (BDA) with Boronated Specific Residues: New Perspectives in Boron Neutron Capture Therapy from an In Silico Investigation.

Authors:  Alessandro Rondina; Paola Fossa; Alessandro Orro; Luciano Milanesi; Antonella De Palma; Davide Perico; Pier Luigi Mauri; Pasqualina D'Ursi
Journal:  Cells       Date:  2021-11-18       Impact factor: 6.600

6.  In Silico Screening of Quorum Sensing Inhibitor Candidates Obtained by Chemical Similarity Search.

Authors:  Sharath Belenahalli Shekarappa; Hrvoje Rimac; Julian Lee
Journal:  Molecules       Date:  2022-07-30       Impact factor: 4.927

7.  Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics.

Authors:  Jorge González-Puelma; Jacqueline Aldridge; Marco Montes de Oca; Mónica Pinto; Roberto Uribe-Paredes; José Fernández-Goycoolea; Diego Alvarez-Saravia; Hermy Álvarez; Gonzalo Encina; Thomas Weitzel; Rodrigo Muñoz; Álvaro Olivera-Nappa; Sergio Pantano; Marcelo A Navarrete
Journal:  Viruses       Date:  2021-05-11       Impact factor: 5.048

8.  The SIRAH-CoV-2 Initiative: A Coarse-Grained Simulations' Dataset of the SARS-CoV-2 Proteome.

Authors:  Pablo G Garay; Exequiel E Barrera; Florencia Klein; Matias R Machado; Martín Soñora; Sergio Pantano
Journal:  Front Med Technol       Date:  2021-02-15

9.  Rolling circle RNA synthesis catalyzed by RNA.

Authors:  Emil Laust Kristoffersen; Matthew Burman; Agnes Noy; Philipp Holliger
Journal:  Elife       Date:  2022-02-02       Impact factor: 8.713

  9 in total

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