Standard equilibration protocols were used (for a detailed description see the Supplementary Data section). The final MD simulations were performed with the PMEMD CUDA version of AMBER12 (68 ,76 ,77 ). The periodic boundary conditions were defined by the PME algorithm and the non-bonded cut-off was set to 9 Å (78 ). Covalent bonds involving hydrogen atoms were constrained using the SHAKE algorithm with a tolerance of 0.0001 Å, allowing integration time step of 2 fs (79 ). All simulations were carried out at a constant pressure of 1 atm and a constant temperature of 300 K. The temperature and pressure were maintained using a Berendsen weak coupling thermostat (80 ). Typically, the frames were written at every 10 ps, so the 10 μs trajectory analyses are based on 106 datapoints (to simplify the Figures, the graphs were prepared using only each 10th snapshot). Analyses of trajectories were performed using the ptraj module of AMBER (81) and the VMD program was used for visualization (82). The programs CHIMERA (www.cgl.ucsf.edu/chimera ) (83 (link)) and PyMOL (www.pymol.org ) (84 ) were also used for visualization. A list of all simulations is given in Table 1 .
Weak coupling thermostat
Manufactured by Berendsen
The Weak Coupling Thermostat is a laboratory equipment designed to precisely regulate and maintain the temperature of a sample or system. It utilizes a mechanism that creates a weak thermal coupling between the sample and the temperature control system, allowing for accurate and stable temperature control.
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Lab products found in correlation
2 protocols using weak coupling thermostat
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Molecular Dynamics Simulation Protocols
2
All-Atom Molecular Dynamics Simulations of Biomolecular Systems
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The starting structures
were equilibrated
using standard protocols (see theSupporting Information ). The final MD simulations were performed with the PMEMD CUDA version
of AMBER12.86 −88 (link) The periodic boundary conditions were defined by
the PME algorithm and the nonbonded cutoff was set to 9 Å.89 (link) Covalent bonds involving hydrogen atoms were
constrained using the SHAKE algorithm with a tolerance of 0.0001 Å,
which allowed us to use an integration time step of 2 fs.90 (link) Simulations8 and 13 –18 were carried out with version AMBER14 using
the hydrogen mass repartitioning of solute atoms and an integration
time step of 4 fs.91 (link) All the simulations
were carried out at constant pressure and temperature of 1 atm and
300 K, respectively. The temperature and pressure were maintained
using the Berendsen weak coupling thermostat.92 (link) The final production run without restraints (unless specified) was
carried out for a continuous 10 μs period (unless specified),
and the frames were written at every 10 ps, so the analyses are based
on 106 data points. Analyses of trajectories were performed
using the cpptraj module of AMBER, and VMD and the
PYMOL programs were used for visualization.93 (link)−95
were equilibrated
using standard protocols (see the
of AMBER12.86 −88 (link) The periodic boundary conditions were defined by
the PME algorithm and the nonbonded cutoff was set to 9 Å.89 (link) Covalent bonds involving hydrogen atoms were
constrained using the SHAKE algorithm with a tolerance of 0.0001 Å,
which allowed us to use an integration time step of 2 fs.90 (link) Simulations
the hydrogen mass repartitioning of solute atoms and an integration
time step of 4 fs.91 (link) All the simulations
were carried out at constant pressure and temperature of 1 atm and
300 K, respectively. The temperature and pressure were maintained
using the Berendsen weak coupling thermostat.92 (link) The final production run without restraints (unless specified) was
carried out for a continuous 10 μs period (unless specified),
and the frames were written at every 10 ps, so the analyses are based
on 106 data points. Analyses of trajectories were performed
using the cpptraj module of AMBER, and VMD and the
PYMOL programs were used for visualization.93 (link)−95
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