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The molecular system was described using internal coordinate variables.
According to the ICM method, the molecular system was described using internal coordinates as variables.
The whole molecular system was subjected to energy minimisations of 500 iterations by a steepest descent algorithm implementing a GROMOS96 43a1 force field.
Each molecular system was then heated to 300 K for 100 ps followed by a 50 ps constant pressure simulation to adjust the density to 1 g/mL.
After this, whole molecular system was subjected to energy minimization for 5000 iterations by steepest descent algorithm implementing GROMOS96 43a1 force field.
This original molecular system was subsequently co-opted by the various contexts of embryogenesis in different eumetazoan phyla, for axis or tissue (see e.g., Di-Poi et al., 2007) patterning, illustrating its remarkable adaptability throughout animal evolution.
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When an equilibrated nuclear, atomic, or molecular system is subjected to an abrupt physical change, such as a sudden rise in temperature or pressure, it takes time for the system to re-equilibrate under the new conditions.
Quantum mechanics predicts probabilities in matter (wave functions); however, the mathematical calculations necessary to describe the probability states for electrons in an atomic or molecular system were far too complex to be useful to scientists.
The continuum temperature to the molecular system is accomplished by an energy transfer scheme.
It is important to choose a level which is well matched with the molecular system being studied.
The first step in building the force field for a given molecular system is assigning correct types to each atom.
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