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

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: amber99sb-ildn using ACE in the N-terminal and COO- in the C-terminal amber99sb-ildn-scaled using ACE in the N-terminal and COO- in the C-terminal charmm36m using ACE in the N-terminal and COO- in the C-terminal charmm36m-scaled using ACE in the N-terminal and COO- in the C-terminal charmm36m using NH2 in the N-terminal and COO- in the C-terminal charmm36m-scaled using NH2 in the N-terminal and COO- in the C-terminal For each of these models we have used the following counterions: Charmm36m - K+ or Na+ original charmm36 counterions Charmm36 (scaled version) - K_s or NA_s scaled counterions Amber99sb-ildn - K+ and Na+ original amber99sb-ildn counterions Amber99sb-ildn (scaled version) - K_s or NA_s scaled counterions Scaled counterions can be found in https://bitbucket.org/hseara/ions/ <strong>MD engine:</strong> gromacs 2018 or 2018.3 or 2018.4 <strong>Temperature</strong>: 300 K <strong>Pressure:</strong> 1 bar <strong>Simulation time</strong>: 1000 ns <strong>Saving frequency</strong>: 100 ps