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The media is considered to be the fourth pillar in a democratic country. It acts as an effective control mechanism to check the other branches of the government. But this is only consequential when the media functions in an independent and transparent fashion with trained and neutral professionals who are aware of the accountability and consequences of their work. All these factors together would further the country as a democratic institution. Traditionally, it was legacy media responsible for a one-to-many communication process. Their goal was to provide information to the citizens. But this changed with development in technology and the use of social media in daily life. The internet brought with it new media formats which are easily accessible but also unstructured. These lowered barriers of entry in the media enabled citizens to become active participants in the communication process. As a result, these citizens developed a different relationship with the already existing media wherein they were not only the receivers to information but also co-producers. Real-time information allows users to communicate with each other and in turn widely generate public opinion on internet platforms. A many-to-many communication style emerged. While on the one hand, this type of discourse could be an opportunity for citizens to exercise their fundamental freedom of speech and expression, it is on the other hand, proving to have a detrimental effect in two parts: Lack of neutrality, polarized views and pre-existing misconceptions on the part of citizens as well as algorithms and formation of echo-chambers on the part of technology. Some questions arise in this scenario about the capability of citizen journalists, the duties they should adhere to along with the enjoyment of their rights and freedoms, the risks involved in an unchecked method of communication and the effect of citizen journalism in the democratic process.
Herein we report an update to ACPYPE, a Python3 tool that now properly converts AMBER to GROMACS topologies for force fields that utilize nondefault and nonuniform 1–4 electrostatic and nonbonded scaling factors or negative dihedral force constants. Prior to this work, ACPYPE only converted AMBER topologies that used uniform, default 1–4 scaling factors and positive dihedral force constants. We demonstrate that the updated ACPYPE accurately transfers the GLYCAM06 force field from AMBER to GROMACS topology files, which employs non-uniform 1–4 scaling factors as well as negative dihedral force constants. Validation was performed using β-d-GlcNAc through gas-phase analysis of dihedral energy curves and probability density functions. The updated ACPYPE retains all of its original functionality, but now allows the simulation of complex glycomolecular systems in GROMACS using AMBER-originated force fields. ACPYPE is available for download at https://github.com/alanwilter/acpype.