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ORCA Program Installation Guide
ORCA, Prof. Frank Neese'nin grubu tarafından geliştirilen güçlü ve çok yönlü bir kuantum kimyası yazılım paketidir. ORCA programı akademik kullanım için ücretsizdir.

Ahmet Güveli
Apr 43 min read


Molecular Dynamics Simulation with AMBER: A Practical Guide – Part 2
In the drug development process, a molecule’s pharmacokinetic properties are as critical as its biological activity. Understanding how a potential drug candidate behaves in the body, whether it reaches the target site at sufficient concentrations, and how long it remains in its bioactive form are fundamental pillars of a successful drug development process.

Ahmet Güveli
Mar 242 min read


Molecular Dynamics Simulation with AMBER: A Practical Guide – Part 1
In the drug development process, a molecule’s pharmacokinetic properties are as critical as its biological activity. Understanding how a potential drug candidate behaves in the body, whether it reaches the target site at sufficient concentrations, and how long it remains in its bioactive form are fundamental pillars of a successful drug development process.

Ahmet Güveli
Mar 65 min read


Time Integration Algorithms in Molecular Dynamics Simulations
Molecular dynamics (MD) simulations are a powerful computational tool for understanding structure–dynamics–function relationships at the atomic level; however, reaching long timescales, especially in large biomolecular systems, entails substantial computational cost. For this reason, numerous “acceleration algorithms” have been developed, ranging from the numerical integration of the equations of motion—forming the foundation of classical MD—to the optimization of force calcu

Emre Can Buluz
Mar 15 min read


Achieving Equilibrium in Molecular Dynamics: Temperature and Pressure Control in NVT and NPT Ensembles
When investigating the behavior of microscopic systems using in silico methods, it is critically important to define the physical conditions under which the system evolves. While energy is conserved in an isolated system (microcanonical ensemble), real experimental conditions are typically open to heat and work exchange with the surrounding environment.

İlayda Boyraz
Feb 84 min read
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