Is there a way to quantify (eg.: plots) the van der waal's or other hydrophobic interactions of a residue through a simulation?
For example, using VMD, we can check for salt-bridges and hydrogen bonds of individual residues through a simulation.
For residues like Phenylalanine or leucine, is there a way to check and generate data for the interactions it is involved in with other residues throughout the length of the simulation?
I have run the simulation on Desmond.
Thanks.
You can make energy groups in gromacs to calculate interaction energies. For more details, check the following tutorial:
http://www.mdtutorials.com/gmx/complex/index.html
Thanks for your replies. I did the simulation using Desmond, not Gromacs. So, how would i calculate the same for a Desmond simulation?
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