
Toppar files for polarizable model based on the classical Drude
oscillator.

August 2014
adm jr.

Includes early Drude toppar files that are not included with the full
Drude release which may be obtained from the MacKerell lab web page.

http://mackerell.umaryland.edu/CHARMM_drude_ff_params.html

The files in this directory and subdirectories are designed based on
the implementation of the polarizable Drude oscillator model in
version c35 and later of charmm.  The input format for the Drude polarizable
model changed significantly upon going from C34 to C35.  The changes
involved placing the majority of the information required to generate
the information to run the Drude model in the RTF file.  This
information may be used in conjunction with the "AUTOgenerate Drudes"
command to create the new polarizable model.  This implementation is
significantly faster than the previous version and is much more
transparent to the user.  In association with these changes
significant alterations in the toppar files to run the Drude
polarizable modele have been made, as described below.  See
doc/Drude.src for more details.

subdirectory positive_drude

This directory contains toppar files based on a positive Drude
particle.  They are maintained for completeness; however, the negative
Drude parameters will be the default in the future.

toppar_drude_positive_swm4_ions.str: toppar information for SWM4-DP
and ions based on a positive Drude.

positive_drude_test_temp.inp: test case for the SWM4-DP and ions. See
the 00readme file for details.

References

Review

Lopes, P.E.M., B. Roux, R., MacKerell, A.D., Jr. “Molecular modeling
and dynamics studies with explicit inclusion of electronic
polarizability. Theory and applications.” Theoretical Chemistry
Accounts, 124:11-28, 2009, PMC2888514

General method

Anisimov, V.M., Lamoureux, G., Vorobyov, I.V., Huang, N.,
Roux, B. and MacKerell, A.D., Jr. :Determination of Electrostatic
Parameters for a Polarizable Force Field Based on the Classical Drude
Oscillator," Journal of Chemical Theory and Computing, 1:153-168,
2005.

Water model (see POSTIVE DRUDE REFERENCES below)

SWM4-NDP, negative Drude (this will be the default model): Lamoureux,
G., Harder, E., Vorobyov, I.V., Deng, Y., Roux, B. MacKerell, A.D.,
Jr., A polarizable model of water for molecular dynamics simulations
of biomolecules, Chemical Physics Letters, 2006, 418: 245-249.

SWM6: Wenbo Yu, Pedro E. M. Lopes, Benoît Roux and Alexander
D. MacKerell, Jr.  "Six-site Polarizable Model of Water Based on the
Classical Drude Oscillator" Journal of Chemical Physics, 138: 034508,
2013

Proteins:

Lopes, P.E.M., Huang, J., Shim, J., Luo, Y., Li, H., Roux, B., and
MacKerell, A.D., Jr., “Polarizable Force Field for Peptides and
Proteins based on the Classical Drude Oscillator,” Journal of Chemical
Theory and Computation, 9: 5430–5449, 2013, 10.1021/ct400781b,
PMC3896220

Nucleic Acids:

Savelyev, A. and MacKerell, A.D., Jr., “All-Atom Polarizable Force
Field for DNA Based on the Classical Drude Oscillator Model,” Journal
of Computational Chemistry, 35: 1219–1239, 2014, DOI:
10.1002/jcc.23611, PMC4075971

Savelyev, A. and MacKerell, A.D., Jr., “Balancing the interactions of
ions, water and DNA in the Drude polarizable force field,” Journal of
Physical Chemistry B, 118: 6742-6757, 2014, 10.1021/jp503469s,
PMC406469

Lipids:

Chowdhary, J., Harder, E., Lopes, P.E.M., MacKerell, Jr., A.D, and
Roux, B., “A Polarizable Model for Phosphatidylcholine-Containing
Biological Membranes,” Journal of Physical Chemistry B.,117:
9142-9160, 2013. PMC3799809

Carbohydrates:

He, X., Lopes, P.E.M., and MacKerell, A.D., Jr., “Polarizable
Empirical Force Field for Acyclic Poly-Alcohols Based on the Classical
Drude Oscillator,” Biopolymers, 99: 724-738, 2013, doi:
10.1002/bip.22286, PMC3902549

Patel, D.S., He, X., and MacKerell, A.D., Jr., “Polarizable Empirical
Force Field for Hexopyranose Monosaccharides based on the Classical
Drude Oscillator,” Journal of Physical Chemistry B., ASAP article,
2014, 10.1021/jp412696m, NIHMSID #566721

Alkanes: 

Igor V. Vorobyov, Victor M. Anisimov and Alexander D. MacKerell,
Jr. "Polarizable Empirical Force Field for Alkanes Based on the
Classical Drude Oscillator Model," Journal of Physical Chemistry B,
109: 18988-18999, 2005.

Anisotropic polarizability model:

Harder, E., Anisimov, V.M., Vorobyov, I.V., Lopes, P.E., Noskov, S.,
MacKerell, A.D., Jr.  and Roux, B. Atomic Level Anisotropy in the
Electrostatic Modeling of Lone Pairs for a Polarizable Force Field
based on the Classical Drude Oscillator, Journal of Chemical Theory
and Computation, 2: 1587-1597, 2006

Ethers:

Vorobyov, I.V., Anisimov, V.M., Greene, S., Venable, R.M., Moser, A.,
Pastor, R.W. and MacKerell, A.D., Jr., Additive and Classical Drude
Polarizable Force Fields for Linear and Cyclic Ethers, Journal of
Chemical Theory and Computation, 3: 1120-1133, 2007.

Baker, C. and MacKerell, Jr. A.D., “Polarizability Rescaling and
atom-based Thole Scaling in the CHARMM Drude Polarizable Force Field
for Ethers” Journal of Molecular Modeling, 16: 567-576, 2010,
PMC2818097

Sulfur containing compounds

Zhu, X. and MacKerell, A.D., Jr. “Polarizable Empirical Force Field
for Sulfur-Containing Compounds Based on the Classical Drude
Oscillator Model,” Journal of Computational Chemistry, 12: 2330-2341,
2010. PMC2923574

Alcohols:

Anisimov, V.M., Vorobyov, I.V., Roux, B., and MacKerell, A.D., Jr.
Polarizable empirical force field for the primary and secondary
alcohol series based on the classical Drude model. Journal of Chemical
Theory and Computation, 3, 1927-1946, 2007.

Amides:

Harder, E., Anisimov, V.M., Whitfield, T., MacKerell, A.D., Jr., Roux,
B. "Understanding the Dielectric Properties of Liquid Amides from a
Polarizable Force Field," Journal of Physical Chemistry,
112:3509-3521. 2008, PMID: 18302362

Amide model used in 2013 protein FF

Lin, B., Lopes, P.E.M., Roux, B., and MacKerell, A.D., Jr.,
“Kirkwood-Buff Analysis of Aqueous N-Methylacetamide and Acetamide
Solutions Modeled by the CHARMM Additive and Drude Polarizable Force
Fields,” Journal of Chemical Physics, 139: 084509, 2013, PMC3772949

Aromatics:

Lopes, P., Lamoureux, G., Roux, B., MacKerell, A.D., Jr., "Polarizable
Empirical Force Field for Aromatic Compounds Based on the Classical
Drude Oscillator," Journal of Physical Chemistry, B. 111:2873-2885,
2007

Heterocycles

Lopes, P.E.M., Lamoureux, G., MacKerell, A.D., Jr., “Polarizable
Empirical Force Field for Nitrogen-containing Heteroaromatic Compounds
Based on the Classical Drude Oscillator” Journal of Computational
Chemistry, 30: 1821-1838, 2009, PMC251901

Nucleic Acid Bases

Baker, C.M., Anisimov, V.M., and MacKerell, A.D., Jr., “Development of
CHARMM Polarizable Force Field for Nucleic Acid Bases Based on the
Classical Drude Oscillator Model,” Journal of Physical Chemistry,
B. 115; 580–596, 2011, PMC3166616

Polyalcohols

He, X., Lopes, P.E.M., and MacKerell, A.D., Jr., “Polarizable
Empirical Force Field for Acyclic Poly-Alcohols Based on the Classical
Drude Oscillator,” Biopolymers, 99: 724-738 2013, DOI:
10.1002/bip.22286

Atomic Ions

Yu, H., Whitfield, T.W., Harder, E., Lamoureux, G., Vorobyov, I.,
Anisimov, V. M., MacKerell, A.D., Jr., and Roux, B. “Simulating
Monovalent and Divalent Ions in Aqueous Solution Using a Drude
Polarizable Force Field, “Journal of Chemical Theory and Computation,
6: 774–786, 2010

Luo, Y., Jiang, W., Yu, H., MacKerell, A.D., Jr., and Roux, B.,
“Simulation study of ion pairing in concentrated aqueous salt
solutions with a polarizable force field,” Faraday Discussions, 160,
135–149, 2013,PMC3695446

POSTIVE DRUDE REFERENCES

SWM4-DP, positive Drude (works with ions of Lamoureux and Roux):
Lamoureux, G., MacKerell, A.D., Jr., Roux, B. "A simple polarizable
model of water based on classical Drude oscillators," Journal of
Chemical Physics, 119: 5185-5197, 2003

Ions

Lamoureux, G.; Roux, B. Absolute Hydration Free Energy Scale for
Alkali and Halide Ions Established from Simulations with a Polarizable
Force Field, J. Phys. Chem. B 2006, 110, 3308
