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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
Charmm36, polyglutamic, polyaspartic, amber99sb-ildn, ECC
Charmm36, polyglutamic, polyaspartic, amber99sb-ildn, ECC
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