Literature DB >> 25081234

Lipid converter, a framework for lipid manipulations in molecular dynamics simulations.

Per Larsson1, Peter M Kasson.   

Abstract

Construction of lipid membrane and membrane protein systems for molecular dynamics simulations can be a challenging process. In addition, there are few available tools to extend existing studies by repeating simulations using other force fields and lipid compositions. To facilitate this, we introduce Lipid Converter, a modular Python framework for exchanging force fields and lipid composition in coordinate files obtained from simulations. Force fields and lipids are specified by simple text files, making it easy to introduce support for additional force fields and lipids. The converter produces simulation input files that can be used for structural relaxation of the new membranes.

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Year:  2014        PMID: 25081234      PMCID: PMC4266579          DOI: 10.1007/s00232-014-9705-5

Source DB:  PubMed          Journal:  J Membr Biol        ISSN: 0022-2631            Impact factor:   1.843


  21 in total

1.  Structural information from multilamellar liposomes at full hydration: full q-range fitting with high quality x-ray data.

Authors:  G Pabst; M Rappolt; H Amenitsch; P Laggner
Journal:  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics       Date:  2000-09

2.  Mechanism of voltage gating in potassium channels.

Authors:  Morten Ø Jensen; Vishwanath Jogini; David W Borhani; Abba E Leffler; Ron O Dror; David E Shaw
Journal:  Science       Date:  2012-04-13       Impact factor: 47.728

3.  CHARMM-GUI: a web-based graphical user interface for CHARMM.

Authors:  Sunhwan Jo; Taehoon Kim; Vidyashankara G Iyer; Wonpil Im
Journal:  J Comput Chem       Date:  2008-08       Impact factor: 3.376

4.  GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit.

Authors:  Sander Pronk; Szilárd Páll; Roland Schulz; Per Larsson; Pär Bjelkmar; Rossen Apostolov; Michael R Shirts; Jeremy C Smith; Peter M Kasson; David van der Spoel; Berk Hess; Erik Lindahl
Journal:  Bioinformatics       Date:  2013-02-13       Impact factor: 6.937

5.  MDAnalysis: a toolkit for the analysis of molecular dynamics simulations.

Authors:  Naveen Michaud-Agrawal; Elizabeth J Denning; Thomas B Woolf; Oliver Beckstein
Journal:  J Comput Chem       Date:  2011-04-15       Impact factor: 3.376

6.  Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types.

Authors:  Jeffery B Klauda; Richard M Venable; J Alfredo Freites; Joseph W O'Connor; Douglas J Tobias; Carlos Mondragon-Ramirez; Igor Vorobyov; Alexander D MacKerell; Richard W Pastor
Journal:  J Phys Chem B       Date:  2010-06-17       Impact factor: 2.991

7.  United Atom Lipid Parameters for Combination with the Optimized Potentials for Liquid Simulations All-Atom Force Field.

Authors:  Jakob P Ulmschneider; Martin B Ulmschneider
Journal:  J Chem Theory Comput       Date:  2009-07-14       Impact factor: 6.006

8.  Lipid Models for United-Atom Molecular Dynamics Simulations of Proteins.

Authors:  Andreas Kukol
Journal:  J Chem Theory Comput       Date:  2009-02-20       Impact factor: 6.006

9.  ACPYPE - AnteChamber PYthon Parser interfacE.

Authors:  Alan W Sousa da Silva; Wim F Vranken
Journal:  BMC Res Notes       Date:  2012-07-23

10.  Derivation and systematic validation of a refined all-atom force field for phosphatidylcholine lipids.

Authors:  Joakim P M Jämbeck; Alexander P Lyubartsev
Journal:  J Phys Chem B       Date:  2012-03-01       Impact factor: 2.991

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  1 in total

1.  Simulation Best Practices for Lipid Membranes [Article v1.0].

Authors:  David J Smith; Jeffery B Klauda; Alexander J Sodt
Journal:  Living J Comput Mol Sci       Date:  2019-01-09
  1 in total

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