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

Simulations of polyglutamic and polyaspartic oligopeptides of 32 amino acids in solution with only counterions (Na+ or K+). For each oligopeptide we have simulated:

• Charmm36 - "c" using either K+ and Na+ original counterions
• Charmm36 (scaled version) - "sc" using either K_s or NA_s scaled counterions
• Amber99sb-ildn - "a" using either K+ and Na+ original counterions
• Amber99sb-ildn (scaled version) - "sa" - using either K_s or NA_s scaled counterions

Scaled counterions can be found in  https://bitbucket.org/hseara/ions/

Amber99sb-ildn oligopeptides: 32 aminoacids (ASP or GLU) with ACE in the N-terminal and COO- in the C-terminal.

Charmm36 oligopeptides: 32 amino acids (ASP or GLU) with NH2 in the N-Terminal and COO- in the C-terminal.

MD engine: gromacs 2018 or 2018.3

Temperature: 300 K

Pressure: 1 bar

Simulation time: 1000 ns

Saving frequency: 100 ps