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Systems were equilibrated for approximately 400 ps by position restrained MD at 300K to eliminate remaining repulsive energies.
Following initial energy minimization and a 100-ps MD run, during which the protein atoms were position restrained, the temperature of solute and solvent was raised from 50 to 300 K in a stepwise manner.
A 1 ns position restrained run in the isothermal isobaric ensemble was then performed using the Berendsen weak coupling algorithm.
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We extend the study of thermophoresis in nanotechnology from the continuous linear motion of nanoparticles that has been actively studied to the position restraining of nanoparticles by designing a one-dimensional thermal potential barrier.
Such lack of sound knowledge about what is really calculated in background may lead to incorrect settings and/or results: insufficient time for energy minimisation and position restraining, too short cut offs, water shells with inappropriate sizes et cetera.
A preliminary MD (1 ns) with heavy atom positions restrained was performed to achieve solvent equilibration and system heating to 310 K.
During MD simulations, ARGRGD and ASPα218 position restrains were removed, and center of mass rotation and translation of the receptor were restrained.
For this, the animals were maintained on quadrupedal position, physically restrained and sedated with 0.5 mg kg−1 xylazine (Sedomin®, Koning, ARG).
A numerical code, named COUPLE, has been developed for computing the motions and tensions pertaining to a moored floating structure positioned and restrained by its mooring/tendon and riser systems.
The European powers, locked in war, were in no position to restrain Japan, and the United States was unwilling to intervene.
A slight change of the pump laser beam position dramatically restrains the main peak and increases the neighboring multiple peak intensity.
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