Molecular Dynamics Simulations of C2 fragment of protein G in solution

Published: 12-03-2018| Version 1 | DOI: 10.17632/9kdc9w6nbc.1
Hiqmet Kamberaj


This data shows the MD simulation configuration snapshots saved every picoseconds for the C2 fragment of protein G in solution. The simulation length was 30 ns. TIP3P was used to model the water molecules, and a salt concentration of 154 mM NaCl was added into solution. Periodic boundary conditions were used with Particle-Mesh Ewald method to handle long-range electrostatics. A cutoff of 12 Angstroms were used for non-bonded interactions. The SHAKE algorithms was used to constraint the hydrogen covalent bonds and the numerical integration time step was 2 femtoseconds.