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The stability of the systems was studied by molecular dynamics simulation with the further analysis of the time dependent root-mean-square coordinate deviation (RMSD) from the initial structure, and temperature factors.
The PRF is then used to approximate the angular-dependent root-mean-square resolution in the directions parallel and perpendicular to the tilt of the point source.
The time-dependent evolution of the root mean square deviations (RMSD) for the peptide α-Cs, radius of gyration and secondary structure (i.e., analyzed using the DSSP criteria [72] for the peptide in the HFIP-water environment indicated when equilibrium was reached. Molecular model structures were rendered using Rasmol version 2.7.4.2 (http://www.RasMol.org) and PyMOL v0.99 (http://www.pymol.org).org
Results show that matric potential-dependent bias was reduced significantly while root mean square error (RMSE) for water content were reduced modestly; RMSE for Ks was increased by 0.9% (H3w) to 3.3% (H5w) in the new models on log scale of Ks compared with the Rosetta1 model.
The TMD methodology imposes a time-dependent holonomic or harmonic constraint on the RMSD (root mean square deviation) in order to drive the system to a target structure.
Rq = root mean square roughness.
The root mean square (r.m.s).
(root mean square) and peak displacements, respectively.
A root mean square error of 0.6 °C was obtained.
All models gave similar root mean square error values.
Root mean square error was found out as 1.56.
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