Dear all. Is there a way to simulate temperature or voltage treatments to a single protein? If so, is there an online web server to conduct it or using BioVia Discovery/AutoDock tools? Thanks in advance for your answers.
Hi Ivan Luzardo-Ocampo ,
You can try Gromacs for the same
Tutorial: (http://www.mdtutorials.com/gmx/)
Exactly, the temperature is an inherent property of MD simulations but for a voltage treatment, I think you would need to use a transmembrane protein, which you should embed in a membrane. Then you should create an imbalance of positive/negative ions across the membrane which will give you an electric potential difference i.e. Voltage.
You can use this to study the conductance of ion channels as we have done in this example:
Article Identification of a cation transport pathway in Neisseria me...
See if this helps you: https://ambermd.org/tutorials/advanced/tutorial33/index.htm
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