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Title: CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

Abstract

Here we report that proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find the optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocol used in CHARMM as well as from experiments. The optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as wellmore » as with experimental data. AMBER compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the LJ potential versus a force-based switching function used to smooth the LJ potential as it approaches the cutoff distance. The optimal simulation protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.« less

Authors:
 [1];  [1];  [2];  [3];  [4];  [5];  [6];  [6];  [7];  [1];  [8];  [4];  [2];  [6];  [5];  [9];  [1]
  1. Univ. of Kansas, Lawrence, KS (United States). Dept. of Molecular Biosciences and Center for Computational Biology
  2. Rutgers Univ., Piscataway, NJ (United States). Dept. of Chemistry and Chemical Biology
  3. Korean Inst. of Science and Technology Information, Daejeon (Korea)
  4. Stanford Univ., CA (United States). Dept. of Bioengineering
  5. Univ. of Maryland, College Park, MD (United States). Dept. of Pharmaceutical Sciences
  6. Univ. of Michigan, Ann Arbor, MI (United States). Dept. of Chemistry
  7. Harvard Medical School, Boston, MA (United States). Cancer Research Inst.
  8. Argonne National Lab. (ANL), Argonne, IL (United States)
  9. Univ. of Maryland, College Park, MD (United States). Dept. of Chemical and Biomolecular Engineering
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE; National Science Foundation (NSF); National Institutes of Health (NIH)
OSTI Identifier:
1261132
Grant/Contract Number:  
DBI-1145652; DBI-1145987; MCB-1149187; MCB-1157677; F32GM109632; GM037554; GM051501; GM070855; GM103695; R01GM072558; U54GM087519; KSC-2015-C3-004
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Journal of Chemical Theory and Computation
Additional Journal Information:
Journal Volume: 12; Journal Issue: 1; Journal ID: ISSN 1549-9618
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING

Citation Formats

Lee, Jumin, Cheng, Xi, Swails, Jason M., Yeom, Min Sun, Eastman, Peter K., Lemkul, Justin A., Wei, Shuai, Buckner, Joshua, Jeong, Jong Cheol, Qi, Yifei, Jo, Sunhwan, Pande, Vijay S., Case, David A., Brooks, Charles L., MacKerell, Alexander D., Klauda, Jeffery B., and Im, Wonpil. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. United States: N. p., 2015. Web. doi:10.1021/acs.jctc.5b00935.
Lee, Jumin, Cheng, Xi, Swails, Jason M., Yeom, Min Sun, Eastman, Peter K., Lemkul, Justin A., Wei, Shuai, Buckner, Joshua, Jeong, Jong Cheol, Qi, Yifei, Jo, Sunhwan, Pande, Vijay S., Case, David A., Brooks, Charles L., MacKerell, Alexander D., Klauda, Jeffery B., & Im, Wonpil. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. United States. https://doi.org/10.1021/acs.jctc.5b00935
Lee, Jumin, Cheng, Xi, Swails, Jason M., Yeom, Min Sun, Eastman, Peter K., Lemkul, Justin A., Wei, Shuai, Buckner, Joshua, Jeong, Jong Cheol, Qi, Yifei, Jo, Sunhwan, Pande, Vijay S., Case, David A., Brooks, Charles L., MacKerell, Alexander D., Klauda, Jeffery B., and Im, Wonpil. 2015. "CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field". United States. https://doi.org/10.1021/acs.jctc.5b00935. https://www.osti.gov/servlets/purl/1261132.
@article{osti_1261132,
title = {CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field},
author = {Lee, Jumin and Cheng, Xi and Swails, Jason M. and Yeom, Min Sun and Eastman, Peter K. and Lemkul, Justin A. and Wei, Shuai and Buckner, Joshua and Jeong, Jong Cheol and Qi, Yifei and Jo, Sunhwan and Pande, Vijay S. and Case, David A. and Brooks, Charles L. and MacKerell, Alexander D. and Klauda, Jeffery B. and Im, Wonpil},
abstractNote = {Here we report that proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find the optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocol used in CHARMM as well as from experiments. The optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as well as with experimental data. AMBER compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the LJ potential versus a force-based switching function used to smooth the LJ potential as it approaches the cutoff distance. The optimal simulation protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.},
doi = {10.1021/acs.jctc.5b00935},
url = {https://www.osti.gov/biblio/1261132}, journal = {Journal of Chemical Theory and Computation},
issn = {1549-9618},
number = 1,
volume = 12,
place = {United States},
year = {Thu Nov 12 00:00:00 EST 2015},
month = {Thu Nov 12 00:00:00 EST 2015}
}

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Binding site opening by loop C shift and chloride ion-pore interaction in the GABA A receptor model
journal, January 2017


Na + coordination at the Na2 site of the Na + /I symporter
journal, August 2016


Phosphoantigen-induced conformational change of butyrophilin 3A1 (BTN3A1) and its implication on Vγ9Vδ2 T cell activation
journal, August 2017


Investigating dual Ca2+ modulation of the ryanodine receptor 1 by molecular dynamics simulation
posted_content, August 2019


A two-lane mechanism for selective biological ammonium transport
journal, November 2019


Structural characterization of a prolyl aminodipeptidase (PepX) from Lactobacillus helveticus
journal, September 2019


Mechanism of homodimeric cytokine receptor activation and dysregulation by oncogenic mutations
journal, February 2020


Effect of Ca2+ on the promiscuous target-protein binding of calmodulin
journal, April 2018


An Unusual Amino Acid Substitution Within Hummingbird Cytochrome c Oxidase Alters a Key Proton-Conducting Channel
journal, July 2020


Magainin 2 and PGLa in Bacterial Membrane Mimics I: Peptide-Peptide and Lipid-Peptide Interactions
journal, November 2019


Homology modeling of human histone deacetylase 10 and design of potential selective inhibitors
journal, January 2019


SurA is a “Groove-y” Chaperone That Expands Unfolded Outer Membrane Proteins
posted_content, August 2020


Correction: A refined model of claudin-15 tight junction paracellular architecture by molecular dynamics simulations
journal, February 2018


Backbone and methyl assignment of bacteriorhodopsin incorporated into nanodiscs
text, January 2020


Investigating dual Ca 2+ modulation of the ryanodine receptor 1 by molecular dynamics simulation
journal, July 2020


A New Computational Method for Membrane Compressibility: Bilayer Mechanical Thickness Revisited
journal, February 2019


Water for Sterol: an Unusual Mechanism of Sterol Egress from a StARkin Domain
journal, February 2020


A two-lane mechanism for selective biological ammonium transport
journal, July 2020


Discovering the chloride pathway in the CFTR channel
journal, July 2019


Comparing pharmacophore models derived from crystal structures and from molecular dynamics simulations
journal, February 2016


Backbone and methyl assignment of bacteriorhodopsin incorporated into nanodiscs
journal, November 2019


Systematic Coarse-Grained Lipid Force Fields with Semiexplicit Solvation via Virtual Sites
journal, January 2019


Substrate-Specific Inhibition Constants for Phospholipase A2 Acting on Unique Phospholipid Substrates in Mixed Micelles and Membranes Using Lipidomics
journal, January 2019


Unidirectional Transport Mechanism in an ATP Dependent Exporter
journal, March 2017


Molecular Basis of the Glucose Transport Mechanism in Plants
journal, May 2019


Virtual Screening of Chemical Compounds for Discovery of Complement C3 Ligands
journal, June 2018


Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand
journal, May 2017


An inner activation gate controls TMEM16F phospholipid scrambling
journal, April 2019


L amino acid transporter structure and molecular bases for the asymmetry of substrate interaction
journal, April 2019


Molecular mechanism of a potassium channel gating through activation gate-selectivity filter coupling
journal, November 2019


Publisher Correction: Hydrophobic gating in BK channels
journal, September 2020


Temporin L and aurein 2.5 have identical conformations but subtly distinct membrane and antibacterial activities
journal, July 2019


The Role of a Crystallographically Unresolved Cytoplasmic Loop in Stabilizing the Bacterial Membrane Insertase YidC2
journal, October 2019


Integrated solid-state NMR and molecular dynamics modeling determines membrane insertion of human β-defensin analog
journal, November 2019


New Insights on Signal Propagation by Sensory Rhodopsin II/Transducer Complex
journal, February 2017


Characterizing the structural ensemble of γ-secretase using a multiscale molecular dynamics approach
journal, January 2017


Na + coordination at the Na2 site of the Na + /I symporter
journal, August 2016


The allosteric mechanism of substrate-specific transport in SLC6 is mediated by a volumetric sensor
journal, July 2019


Membrane perforation by the pore-forming toxin pneumolysin
journal, June 2019


Ensemble-based evaluation for protein structure models
journal, June 2016


Modulation of the helical properties of DNA: next-to-nearest neighbour effects and beyond
journal, April 2019


Self-assembly Controls Self-cleavage of HHR from ASBVd(-): a Combined SANS and Modeling Study
journal, March 2016


Markov modeling reveals novel intracellular modulation of the human TREK-2 selectivity filter
journal, December 2016


Developing a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein Model in a Viral Membrane
journal, June 2020


Understanding the Functional Properties of Lipid Heterogeneity in Pulmonary Surfactant Monolayers at the Atomistic Level
journal, July 2020


β11-12 linker isomerization governs Acid-sensing ion channel desensitization and recovery
posted_content, August 2019


Reduced level of docosahexaenoic acid shifts GPCR neuroreceptors to less ordered membrane regions
journal, May 2019


A refined model of claudin-15 tight junction paracellular architecture by molecular dynamics simulations
journal, September 2017


Augmenting the antinociceptive effects of nicotinic acetylcholine receptor activity through lynx1 modulation
journal, July 2018


Drug-induced diabetes type 2: In silico study involving class B GPCRs
journal, January 2019


Effect of pressure profile of shock waves on lipid membrane deformation
journal, February 2019


Molecular Modeling of Structures and Interaction of Human Corticotropin-Releasing Factor (CRF) Binding Protein and CRF Type-2 Receptor
journal, February 2018


Towards A Molecular Understanding of The Cannabinoid Related Orphan Receptor GPR18: A Focus on Its Constitutive Activity
journal, May 2019


Chirality-Dependent Adsorption between Amphipathic Peptide and POPC Membrane
journal, September 2019


Inhibition of a Snake Venom Metalloproteinase by the Flavonoid Myricetin
journal, October 2018


NFBTA: A Potent Cytotoxic Agent against Glioblastoma
journal, June 2019


Interactions between Triterpenes and a P-I Type Snake Venom Metalloproteinase: Molecular Simulations and Experiments
journal, September 2018


Comparison of Sampling Methods via Robust Free Energy Inference: Application to Calmodulin
preprint, January 2017


Exchange of water for sterol underlies sterol egress from a StARkin domain
journal, December 2019


A novel proton transfer mechanism in the SLC11 family of divalent metal ion transporters.
text, January 2017