Literature DB >> 26781073

LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields.

Eric G Kratz1, Alice R Walker1, Louis Lagardère2,3, Filippo Lipparini4, Jean-Philip Piquemal2, G Andrés Cisneros1.   

Abstract

We introduce an initial implementation of the LICHEM software package. LICHEM can interface with Gaussian, PSI4, NWChem, TINKER, and TINKER-HP to enable QM/MM calculations using multipolar/polarizable force fields. LICHEM extracts forces and energies from unmodified QM and MM software packages to perform geometry optimizations, single-point energy calculations, or Monte Carlo simulations. When the QM and MM regions are connected by covalent bonds, the pseudo-bond approach is employed to smoothly transition between the QM region and the polarizable force field. A series of water clusters and small peptides have been employed to test our initial implementation. The results obtained from these test systems show the capabilities of the new software and highlight the importance of including explicit polarization.
© 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Entities:  

Keywords:  AMOEBA; QM/MM; multipoles; polarization; pseudo-bond

Mesh:

Year:  2016        PMID: 26781073      PMCID: PMC4808410          DOI: 10.1002/jcc.24295

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  69 in total

1.  Solvation Effects on Electronic Transitions: Exploring the Performance of Advanced Solvent Potentials in Polarizable Embedding Calculations.

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Journal:  J Chem Theory Comput       Date:  2011-06-01       Impact factor: 6.006

2.  A critical evaluation of different QM/MM frontier treatments with SCC-DFTB as the QM method.

Authors:  P H König; M Hoffmann; Th Frauenheim; Q Cui
Journal:  J Phys Chem B       Date:  2005-05-12       Impact factor: 2.991

3.  Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface.

Authors:  Hao Hu; Zhenyu Lu; Jerry M Parks; Steven K Burger; Weitao Yang
Journal:  J Chem Phys       Date:  2008-01-21       Impact factor: 3.488

4.  Tests of an adaptive QM/MM calculation on free energy profiles of chemical reactions in solution.

Authors:  Csilla Várnai; Noam Bernstein; Letif Mones; Gábor Csányi
Journal:  J Phys Chem B       Date:  2013-09-27       Impact factor: 2.991

5.  Analytic energy gradients in combined second order Møller-Plesset perturbation theory and conductorlike polarizable continuum model calculation.

Authors:  Dejun Si; Hui Li
Journal:  J Chem Phys       Date:  2011-10-14       Impact factor: 3.488

6.  A second generation distributed point polarizable water model.

Authors:  Revati Kumar; Fang-Fang Wang; Glen R Jenness; Kenneth D Jordan
Journal:  J Chem Phys       Date:  2010-01-07       Impact factor: 3.488

7.  Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model.

Authors:  Marie L Laury; Lee-Ping Wang; Vijay S Pande; Teresa Head-Gordon; Jay W Ponder
Journal:  J Phys Chem B       Date:  2015-02-26       Impact factor: 2.991

8.  The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins.

Authors:  Yue Shi; Zhen Xia; Jiajing Zhang; Robert Best; Chuanjie Wu; Jay W Ponder; Pengyu Ren
Journal:  J Chem Theory Comput       Date:  2013       Impact factor: 6.006

9.  GEM*: A Molecular Electronic Density-Based Force Field for Molecular Dynamics Simulations.

Authors:  Robert E Duke; Oleg N Starovoytov; Jean-Philip Piquemal; G Andrés Cisneros
Journal:  J Chem Theory Comput       Date:  2014-03-03       Impact factor: 6.006

10.  A gauge invariant multiscale approach to magnetic spectroscopies in condensed phase: general three-layer model, computational implementation and pilot applications.

Authors:  Filippo Lipparini; Chiara Cappelli; Vincenzo Barone
Journal:  J Chem Phys       Date:  2013-06-21       Impact factor: 3.488

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  21 in total

1.  An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

Authors:  Jing Huang; Ye Mei; Gerhard König; Andrew C Simmonett; Frank C Pickard; Qin Wu; Lee-Ping Wang; Alexander D MacKerell; Bernard R Brooks; Yihan Shao
Journal:  J Chem Theory Comput       Date:  2017-01-24       Impact factor: 6.006

Review 2.  Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics.

Authors:  A T Hagler
Journal:  J Comput Aided Mol Des       Date:  2018-11-30       Impact factor: 3.686

3.  A Many-Body, Fully Polarizable Approach to QM/MM Simulations.

Authors:  Eleftherios Lambros; Filippo Lipparini; Gerardo Andrés Cisneros; Francesco Paesani
Journal:  J Chem Theory Comput       Date:  2020-11-19       Impact factor: 6.006

4.  Mapping the Drude polarizable force field onto a multipole and induced dipole model.

Authors:  Jing Huang; Andrew C Simmonett; Frank C Pickard; Alexander D MacKerell; Bernard R Brooks
Journal:  J Chem Phys       Date:  2017-10-28       Impact factor: 3.488

5.  Predicting partition coefficients of drug-like molecules in the SAMPL6 challenge with Drude polarizable force fields.

Authors:  Ye Ding; You Xu; Cheng Qian; Jinfeng Chen; Jian Zhu; Houhou Huang; Yi Shi; Jing Huang
Journal:  J Comput Aided Mol Des       Date:  2020-01-20       Impact factor: 3.686

6.  Long-range electrostatic corrections in multipolar/polarizable QM/MM simulations.

Authors:  Eric G Kratz; Robert E Duke; G Andrés Cisneros
Journal:  Theor Chem Acc       Date:  2016-06-17       Impact factor: 1.702

7.  LICHEM 1.1: Recent Improvements and New Capabilities.

Authors:  Hatice Gökcan; Erik Antonio Vázquez-Montelongo; G Andrés Cisneros
Journal:  J Chem Theory Comput       Date:  2019-04-02       Impact factor: 6.006

8.  Ground State Destabilization in Uracil DNA Glycosylase: Let's Not Forget "Tautomeric Strain" in Substrates.

Authors:  Ranjita Das; Erik A Vázquez-Montelongo; G Andrés Cisneros; Judy I Wu
Journal:  J Am Chem Soc       Date:  2019-08-26       Impact factor: 15.419

9.  QM/MM Simulations with the Gaussian Electrostatic Model: A Density-based Polarizable Potential.

Authors:  Hatice Gökcan; Eric Kratz; Thomas A Darden; Jean-Philip Piquemal; G Andrés Cisneros
Journal:  J Phys Chem Lett       Date:  2018-05-23       Impact factor: 6.475

10.  A simplified charge projection scheme for long-range electrostatics in ab initio QM/MM calculations.

Authors:  Xiaoliang Pan; Kwangho Nam; Evgeny Epifanovsky; Andrew C Simmonett; Edina Rosta; Yihan Shao
Journal:  J Chem Phys       Date:  2021-01-14       Impact factor: 3.488

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