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

Authors: Martinez-Seara, Hector;

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

Abstract

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

Keywords

Charmm36, polyglutamic, polyaspartic, amber99sb-ildn, ECC

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
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