Literature DB >> 20649318

Optimizing working parameters of the smooth particle mesh Ewald algorithm in terms of accuracy and efficiency.

Han Wang1, Florian Dommert, Christian Holm.   

Abstract

We construct an accurate error estimate for the root mean square force error of the smooth particle mesh Ewald (SPME) algorithm, which is often used for molecular dynamics simulations, where charge configurations under periodic boundary conditions require considerable amounts of CPU time. The error estimates are provided for the ik- as well as analytical force differentiation schemes, and their validity is tested for a random homogeneous sample system. Finally, we demonstrate that it is possible to straightforwardly and precisely determine the SPME parameters via the error estimates prior to the simulation for a predetermined accuracy. This can save precious computer and user time and allows an easy choice of a suitable parameter set for nearly optimal speed.

Year:  2010        PMID: 20649318     DOI: 10.1063/1.3446812

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  31 in total

Review 1.  Classical electrostatics for biomolecular simulations.

Authors:  G Andrés Cisneros; Mikko Karttunen; Pengyu Ren; Celeste Sagui
Journal:  Chem Rev       Date:  2013-08-27       Impact factor: 60.622

2.  Exploring the mechanistic insights of Cas scaffolding protein family member 4 with protein tyrosine kinase 2 in Alzheimer's disease by evaluating protein interactions through molecular docking and dynamic simulations.

Authors:  Mubashir Hassan; Saba Shahzadi; Hany Alashwal; Nazar Zaki; Sung-Yum Seo; Ahmed A Moustafa
Journal:  Neurol Sci       Date:  2018-05-22       Impact factor: 3.307

3.  Hypothesis driven single nucleotide polymorphism search (HyDn-SNP-S).

Authors:  Rebecca J Swett; Angela Elias; Jeffrey A Miller; Gregory E Dyson; G Andrés Cisneros
Journal:  DNA Repair (Amst)       Date:  2013-07-05

4.  Exploration of Potential Ewing Sarcoma Drugs from FDA-Approved Pharmaceuticals through Computational Drug Repositioning, Pharmacogenomics, Molecular Docking, and MD Simulation Studies.

Authors:  Mubashir Hassan; Muhammad Yasir; Saba Shahzadi; Andrzej Kloczkowski
Journal:  ACS Omega       Date:  2022-06-01

5.  Disruption of intrinsic motions as a mechanism for enzyme inhibition.

Authors:  Rebecca J Swett; G Andrés Cisneros; Andrew L Feig
Journal:  Biophys J       Date:  2013-07-16       Impact factor: 4.033

6.  A novel guaiane sesquiterpene derivative, guai-2-en-10α-ol, from Ulva fasciata Delile inhibits EGFR/PI3K/Akt signaling and induces cytotoxicity in triple-negative breast cancer cells.

Authors:  T Pragna Lakshmi; S Vajravijayan; Mondal Moumita; Natarajan Sakthivel; K Gunasekaran; Ramadas Krishna
Journal:  Mol Cell Biochem       Date:  2017-08-01       Impact factor: 3.396

7.  Identification of novel tyrosine kinase inhibitors for drug resistant T315I mutant BCR-ABL: a virtual screening and molecular dynamics simulations study.

Authors:  Hemanth Naick Banavath; Om Prakash Sharma; Muthuvel Suresh Kumar; R Baskaran
Journal:  Sci Rep       Date:  2014-11-10       Impact factor: 4.379

8.  Flurbiprofen-antioxidant mutual prodrugs as safer nonsteroidal anti-inflammatory drugs: synthesis, pharmacological investigation, and computational molecular modeling.

Authors:  Zaman Ashraf; Munazza Kanwal; Mubashir Hassan; Sahar Abdullah; Mamuna Waheed; Haseeb Ahsan; Song Ja Kim
Journal:  Drug Des Devel Ther       Date:  2016-07-27       Impact factor: 4.162

9.  Mechanistic insights into TNFR1/MADD death domains in Alzheimer's disease through conformational molecular dynamic analysis.

Authors:  Mubashir Hassan; Sara Zahid; Hany Alashwal; Andrzej Kloczkowski; Ahmed A Moustafa
Journal:  Sci Rep       Date:  2021-06-10       Impact factor: 4.379

10.  Conformational analysis of Clostridium difficile toxin B and its implications for substrate recognition.

Authors:  Rebecca Swett; G Andrés Cisneros; Andrew L Feig
Journal:  PLoS One       Date:  2012-07-23       Impact factor: 3.240

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