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/

MD engine: gromacs 2018 or 2018.3 or 2018.4

Temperature: 300 K

Pressure: 1 bar

Simulation time: 1000 ns

Saving frequency: 100 ps