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About Tutorial 1
The document provides instructions for simulating a box of water molecules using the Amber molecular simulation package. It describes: 1) Creating topology and coordinate files for the water box system and a single water molecule using tleap. 2) Performing energy minimization on the water box system using pmemd.MPI to optimize the system and remove clashes. 3) Heating the minimized water box system to room temperature using Langevin dynamics in pmemd.MPI to gradually increase the temperature over 10,000 steps. 4) Equilibrating the heated water box system under constant NVT conditions for 25,000 steps using a Berendsen barostat to adjust the system pressure to 1 atm
Detailed Information
| Author: | ['Witold Szejgis'] |
|---|---|
| Publication Year: | 2017 |
| Pages: | 11 |
| Language: | English |
| Format: | |
| Price: | FREE |
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