Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion

2021 ◽  
Vol 17 (3) ◽  
pp. 1562-1580 ◽  
Author(s):  
Yalun Yu ◽  
Andreas Krämer ◽  
Richard M. Venable ◽  
Andrew C. Simmonett ◽  
Alexander D. MacKerell ◽  
...  
Keyword(s):  
Force Field ◽  
Long Range ◽  
Automated Optimization

A refined polarizable water model for the coarse-grained MARTINI force field with long-range electrostatic interactions

2017 ◽  
Vol 146 (5) ◽  
pp. 054501 ◽  
Author(s):  
Julian Michalowsky ◽  
Lars V. Schäfer ◽  
Christian Holm ◽  
Jens Smiatek
Keyword(s):  
Force Field ◽  
Long Range ◽  
Electrostatic Interactions ◽  
Coarse Grained ◽  
Water Model ◽  
Martini Force Field

Fast Electrostatic Force and Moment Calculations in Multibody-Based Simulations of Coarse-Grained Biopolymers

2011 ◽  
Author(s):  
Mohammad Poursina ◽  
Jeremy Laflin ◽  
Kurt S. Anderson
Keyword(s):  
Force Field ◽  
Long Range ◽  
Electrostatic Force ◽  
Center Of Mass ◽  
Computational Cost ◽  
Field Approximation ◽  
The Body ◽  
Divide And Conquer ◽  
Coarse Grained ◽  
Coarse Grain

In molecular simulations, the dominant portion of the computational cost is associated with force field calculations. Herein, we extend the approach used to approximate long range gravitational force and the associated moment in spacecraft dynamics to the coulomb forces present in coarse grained biopolymer simulations. We approximate the resultant force and moment for long-range particle-body and body-body interactions due to the electrostatic force field. The resultant moment approximated here is due to the fact that the net force does not necessarily act through the center of mass of the body (pseudoatom). This moment is considered in multibody-based coarse grain simulations while neglected in bead models which use particle dynamics to address the dynamics of the system. A novel binary divide and conquer algorithm (BDCA) is presented to implement the force field approximation. The proposed algorithm is implemented by considering each rigid/flexible domain as a node of the leaf level of the binary tree. This substructuring strategy is well suited to coarse grain simulations of chain biopolymers using an articulated multibody approach.

SIRAH: A Structurally Unbiased Coarse-Grained Force Field for Proteins with Aqueous Solvation and Long-Range Electrostatics

2015 ◽  
Vol 11 (2) ◽  
pp. 723-739 ◽  
Author(s):  
Leonardo Darré ◽  
Matías Rodrigo Machado ◽  
Astrid Febe Brandner ◽  
Humberto Carlos González ◽  
Sebastián Ferreira ◽  
...  
Keyword(s):  
Force Field ◽  
Long Range ◽  
Coarse Grained ◽  
Aqueous Solvation

Gitterschwingungsspektren

1976 ◽  
Vol 31 (7) ◽  
pp. 847-852 ◽  
Author(s):  
H. D. Lutz ◽  
P. Willich ◽  
H. Haeuseler
Keyword(s):  
Force Field ◽  
Long Range ◽  
Force Constants ◽  
The Other ◽  
Valence Force ◽  
Normal Coordinates ◽  
Valence Force Field ◽  
Symmetry Coordinates ◽  
Ir Frequencies ◽  
Good Agreement

Abstract Force constants and normal coordinates of MnS2 , FeS2 , RuS2, RuSe2, RuTe2, OsS2 and PtP2 are calculated based on the five ir active vibrations of the pyrite lattice. By setting up a valence force field consisting of short and long range M -X, X2 -X2 and M -M stretching constants it has proved possible to obtain good agreement between experimental and calculated frequencies with expection of FeS2 and RuS2 . The force constants corresponding to the shortest metal chalcogen distances (MnS2: 0.30, RuSe2: 0.88, RuTe2: 0.62, OsS2: 1.32, PtP2: 1.22 mdyn/Å) are mainly responsible for the ir frequencies. For RuSe2 and RuTe2, the forces between adjacent X2 groups are not negligible. Whereas the force constants of OsS2 and PtP2 are of comparable strength, the forces in MnS2 are significantly weaker than those in the other compounds. The normal coordinates of MnS2, OsS2 and PtP2 , and RuSe2 and RuTe2 show significant differences according to both the contribution of the 6 symmetry coordinates to the 5 ir active vibrations and the assignment of the spectra.

HBFF-SVD Force Field Treatment of Ni(II) Porphine:  Important Long Range Cross Terms

2003 ◽  
Vol 107 (4) ◽  
pp. 526-541 ◽  
Author(s):  
Hui-Hsu (Gavin) Tsai ◽  
M. Cather Simpson
Keyword(s):  
Force Field ◽  
Long Range ◽  
Cross Terms

scholarly journals The impact of using single atomistic long range cutoff schemes with the GROMOS 54A7 force field

2019 ◽  
Author(s):  
Tomás Silva ◽  
Diogo Vila-Viçosa ◽  
Pedro Reis ◽  
Bruno Victor ◽  
Matthias Diem ◽  
...  
Keyword(s):  
Force Field ◽  
Long Range ◽  
The Impact
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