Index of papers in March 2015 that mention
  • force field
Lucas A. Defelipe, Esteban Lanzarotti, Diego Gauto, Marcelo A. Marti, Adrián G. Turjanski
Protein structure selection, search parameters and Cys environment characterization
For all residues, except the sulfenic acid, the AMBER99SB force field was used [44,45].
Protein structure selection, search parameters and Cys environment characterization
Sulfenic acid force field parameters were built using AMBER recommended procedure.
Protein structure selection, search parameters and Cys environment characterization
All bonded and VdW parameters were taken from the General AMBER Force Field [47].
force field is mentioned in 3 sentences in this paper.
Topics mentioned in this paper:
Jérôme R. D. Soiné, Christoph A. Brand, Jonathan Stricker, Patrick W. Oakes, Margaret L. Gardel, Ulrich S. Schwarz
Introduction
From this information the traction force field can be reconstructed (Fig 1C) and correlated with the internal actin structure, including actin retrograde flow and SFs [19,20].
Regularlzation
If it is chosen too large, the details of the force field are smoothed out and the overall force magnitude is too small.
Robustness of the method
The deviation between the theoretical prediction and experimental measurement is represented by the relative LZ-norm that ranges between 0 for perfect agreement and 1 for a vanishing force field .
force field is mentioned in 3 sentences in this paper.
Topics mentioned in this paper:
Antreas C. Kalli, Mark S. P. Sansom, Reinhart A. F. Reithmeier
Abstract
Multiscale molecular dynamics simulations of the UraA symporter in phospholipid bilayers consisting of: 1) 1-palmitoyl 2—oIeoyl-phosphatidylcholine (POPC); 2) 1-palmitoyl 2—oleoyI-phosphatidylethanolamine (POPE); and 3) a mixture of 75% POPE, 20% 1-palmi-toyl 2—oleoyl-phosphatidylglycerol (POPG); and 5% 1-palmitoyl 2—oleoyI-diphosphatidylgly-cerol/cardiolipin (CL) to mimic the lipid composition of the bacterial inner membrane, were performed using the MARTINI coarse-grained force field to self-assemble lipids around the crystal structure of this membrane transport protein, followed by atomistic simulations.
Atomistic molecular dynamics simulations
Atomistic molecular dynamics (AT-MD) simulations were performed using the GROMOS96 53a6 force field that has been widely used in simulation studies of membrane proteins.
Coarse-grained molecular dynamics simulations
Coarse-grained molecular dynamics (CG-MD) simulations were performed using the MARTINI force field [22].
force field is mentioned in 3 sentences in this paper.
Topics mentioned in this paper:
Davide Provasi, Mustafa Burak Boz, Jennifer M. Johnston, Marta Filizola
Dynamic Behavior of Lipid Molecules
), corresponding to a lipid diffusion coefficient Dmdz/ (tX) = 10—6 cmZ/s, (or Dm2.5><10_7 cmZ/s, when accounting for the effective time scaling for the CG force field we used).
Dynamic Behavior of Lipid Molecules
Notably, similar values of lipid diffusion constants have recently been reported in the literature [26,27] for comparable CG force fields , and a similar behavior was implied.
System Preparation
The receptors were converted to a CG representation under the MARTINI force field (version 2.1) [16—18] and a modified elastic network was applied, as reported previously in the literature [42].
force field is mentioned in 3 sentences in this paper.
Topics mentioned in this paper: