Simulations of polyglutamic and polyaspartic oligopeptides of 32 amino acids in solution with counterions

<p>Simulations of polyglutamic (GLU32) and polyaspartic (ASP32) oligopeptides of 32 amino acids in solution with only counterions (Na+ or K+). For each oligopeptide we have simulated the following variants:</p> <ul> <li>amber99sb-ildn using ACE in the N-terminal and COO- in the C-terminal</li> <li>amber99sb-ildn-scaled using ACE in the N-terminal and COO- in the C-terminal</li> <li>charmm36m using ACE in the N-terminal and COO- in the C-terminal</li> <li>charmm36m-scaled using ACE in the N-terminal and COO- in the C-terminal</li> <li>charmm36m using NH2 in the N-terminal and COO- in the C-terminal</li> <li>charmm36m-scaled using NH2 in the N-terminal and COO- in the C-terminal</li> </ul> <p>For each of these models we have used the following counterions:</p> <ul> <li>Charmm36m - K+ or Na+ original charmm36 counterions</li> <li>Charmm36 (scaled version) - K_s or NA_s scaled counterions</li> <li>Amber99sb-ildn - K+ and Na+ original amber99sb-ildn counterions</li> <li>Amber99sb-ildn (scaled version) - K_s or NA_s scaled counterions</li> </ul> <p>Scaled counterions can be found in&nbsp; <a href="https://bitbucket.org/hseara/ions/">https://bitbucket.org/hseara/ions/</a></p> <p><strong>MD engine:</strong> gromacs 2018 or 2018.3 or 2018.4</p> <p>&nbsp;</p> <p><strong>Temperature</strong>: 300 K</p> <p>&nbsp;</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 1000 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p>&nbsp;</p>