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Good day, I am working on comparing the deterministic and stochastic trajectories of the polymerization of styrene in free radical reaction. I find it challenging to use the module. How do I obtain a …
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The file format should support common input and output for these applications:
At minimum:
1. Molecular dynamics: simulation (OpenMM, DESMOND, etc.) and analysis packages (MDTraj, PyTraj, etc.)
2. Qu…
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The fastest (but not necessarily least accurate!) method to treat the interaction of a peptide with the cell membrane is via electrostatics. One of the simplest models here is to consider the material…
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Hi Leonardo and community,
I have noticed that the density and velocity structure of the wind can change quite a bit depending on the `initial_f_ion` parameter of the `hydrogen.ion_fraction()` func…
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@doi:10.1021/bi501056h
> We have employed molecular dynamics (MD)
simulation to investigate, with atomic details, the structural dynamics
and energetics of three major ATPase states (ADP, APO, and …
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Defect Description:
The Simulation section of "Familiarization with the fluorescence instrumentation" experiment, once the spectrofluorimeter is switched on the functionality of the lid is not perfor…
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Hello,
I couldn´t understand the impact of the ionic strength in the ∆Gbind calculation for Poisson-Boltzmann. I performed replicates of the same protein:ligand complex and calculated the MMPBSA at…
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Dear Said and colleagues,
I really like the approach of the ModSci ontology. Could you imagine to detail the physics/chemistry section and add terms like x-ray diffraction (XRD), quasi-elastic neut…
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Defect Description:
The Simulation page of "Familiarization with Excitation and Emission Spectra, Mirror Image Relation and Stokes Shift" experiment of this lab, improper alignment is observed for th…
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[Maruca, Annalisa, Francesca Alessandra Ambrosio, Antonio Lupia, Isabella Romeo, Roberta Rocca, Federica Moraca, Carmine Talarico, et al. “Computer-Based Techniques for Lead Identification and Optimiz…