CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations

2003 ◽  
Vol 25 (1) ◽  
pp. 1-16 ◽  
Author(s):  
Sandeep Patel ◽  
Charles L. Brooks
Keyword(s):  
Force Field ◽  
Organic Liquid ◽  
Fluctuating Charge Force Field

Modeling of Cyclic Peptides by the ABEEM/MM Fluctuating Charge Force Field

2006 ◽  
Vol 22 (10) ◽  
pp. 1243-1247
Author(s):  
ZHANG Qiang ◽  
◽  
◽  
ZHANG Xia ◽  
YANG Zhong-Zhi
Keyword(s):  
Force Field ◽  
Cyclic Peptides ◽  
Fluctuating Charge Force Field

MOLECULAR DYNAMICS STUDIES OF CRAMBIN AND BPTI IN TERMS OF ABEEM/MM METHOD

2008 ◽  
Vol 07 (04) ◽  
pp. 697-705 ◽  
Author(s):  
ZHONG-ZHI YANG ◽  
QING-MEI GUAN ◽  
DONG-XIA ZHAO
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Dynamics Simulation ◽  
Dihedral Angles ◽  
Mean Square ◽  
Simulation Studies ◽  
X Ray ◽  
Electronegativity Equalization Method ◽  
Atom Bond ◽  
Fluctuating Charge Force Field

Recently, the ABEEM/MM method (atom-bond electronegativity equalization method fused into molecular mechanics) has successfully been applied to study polypeptide conformations. In order to further test the reliability of this method as well as the transferability of the parameters (including ABEEM and force field parameters), molecular dynamics simulation studies on Crambin and BPTI (298 K, in vacuo) have been performed in terms of ABEEM/MM fluctuating charge force field. Some of their structural properties were obtained, and relative to the X-ray structures, the root-mean-square deviations (RMSD) of bond lengths, bond angles and key dihedral angles, and the coordinate RMSDs of atoms were calculated. The ABEEM/MM results are fairly consistent with those from X-ray experiment.

Millimetre-wave and infrared spectroscopy of Br13 CN: anharmonic force field of cyanogen bromide from spectroscopic data and ab initio calculations

1997 ◽  
Vol 90 (3) ◽  
pp. 495-497
Author(s):  
CLAUDIO ESPOSTI ◽  
FILIPPO TAMASSIA ◽  
CRISTINA PUZZARINI ◽  
RICCARDO TARRONI ◽  
ZDENEK ZELINGER
Keyword(s):  
Infrared Spectroscopy ◽  
Force Field ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Spectroscopic Data ◽  
Cyanogen Bromide ◽  
Millimetre Wave ◽  
Anharmonic Force

Molecular force field evaluation by empirical constraints

1976 ◽  
Vol 73 ◽  
pp. 1051-1057
Author(s):  
Sadao Isotani ◽  
Alain J.-P. Alix
Keyword(s):  
Force Field ◽  
Field Evaluation ◽  
Molecular Force ◽  
Molecular Force Field

Removal of nutrients from Organic Liquid Agricultural Waste using filamentous algae.

2020 ◽  
Author(s):  
Gonzalo Flores-Morales ◽  
Mónica Díaz ◽  
Patricia Arancibia-Avila ◽  
Michelle Muñoz-Carrasco ◽  
Pamela Jara-Zapata ◽  
...  
Keyword(s):  
Organic Waste ◽  
Low Cost ◽  
Organic Liquid ◽  
Agricultural Waste ◽  
Filamentous Algae ◽  
Tertiary Treatment ◽  
Nutrient Reduction ◽  
Algae Removal ◽  
Algae Growth ◽  
Waste Effluents

Abstract A feasibility analysis of tertiary treatment for Organic Liquid Agricultural Waste is presented using filamentous algae belonging to the genus Cladophora sp. as an alternative to chemical tertiary treatment. The main advantages of tertiary treatments that use biological systems are the low cost investment and the minimal dependence on environmental variables. In this work we demonstrate that filamentous algae reduces the nutrient load of nitrate (circa 75%) and phosphate (circa 86%) from the organic waste effluents coming from dairy farms after nine days of culture, with the added advantage being that after the treatment period, algae removal can be achieved by simple procedures. Currently, the organic wastewater is discarded into fields and local streams. However, the algae can acquire value as a by-product since it has various uses as compost, cellulose, and biogas. A disadvantage of this system is that clean water must be used to achieve enough water transparency to allow algae growth. Even so, the nutrient reduction system of the organic effluents proposed is friendly to the ecosystem, compared to tertiary treatments that use chemicals to precipitate and collect nutrients such as nitrates and phosphates.

Optimization of a New Reactive Force Field for Silver - Based Materials

2020 ◽  
Author(s):  
Clément Dulong ◽  
Bruno Madebène ◽  
Susanna Monti ◽  
Johannes Richardi
Keyword(s):  
Force Field ◽  
Self Assembled Monolayers ◽  
The Novel ◽  
Reactive Force ◽  
Reactive Force Field ◽  
Energetic Properties ◽  
Extended Training ◽  
Geometrical Features ◽  
Assembled Monolayers ◽  
Gold Thiolate

<div><div><div><p>A new reactive force field based on the ReaxFF formalism is effectively parametrized against an extended training set of quantum chemistry data (containing more than 120 different structures) to describe accurately silver- and silver-thiolate systems. The results obtained with this novel representation demonstrate that the novel ReaxFF paradigm is a powerful methodology to reproduce more appropriately average geometric and energetic properties of metal clusters and slabs when compared to the earlier ReaxFF parametrizations dealing with silver and gold. ReaxFF cannot describe adequately specific geometrical features such as the observed shorter distances between the under-coordinated atoms at the cluster edges. Geometric and energetic properties of thiolates adsorbed on a silver Ag20 pyramid are correctly represented by the new ReaxFF and compared with results for gold. The simulation of self-assembled monolayers of thiolates on a silver (111) surface does not indicate the formation of staples in contrast to the results for gold-thiolate systems.</p></div></div></div>

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