Simulations Of Polyglutamic And Polyaspartic Oligopeptides Of 32 Amino Acids In Solution With Counterions
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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/ <em>Amber99sb-ildn oligopeptides:</em> 32 aminoacids (ASP or GLU) with ACE in the N-terminal and COO- in the C-terminal. <em>Charmm36 oligopeptides: </em>32 amino acids (ASP or GLU) with NH2 in the N-Terminal and COO- in the C-terminal. <strong>MD engine:</strong> gromacs 2018 or 2018.3 <strong>Temperature</strong>: 300 K <strong>Pressure:</strong> 1 bar <strong>Simulation time</strong>: 1000 ns <strong>Saving frequency</strong>: 100 ps
