So far we're using MD simulation to get RMSD result of the protein-ligand complex and see which one is the best. So far we didn't have the tutorial for doing Thermodynamic Integration MD Simulation for CADDD in GROMACS
Yes. There are some tutorials in Gromacs's website: http://www.gromacs.org/Documentation/Tutorials . See the free energy calculations section.
In principle yes, however you need a lot of data to get adequate sampling of states.
Also, it is hard to say if the claimed thermodynamic results are accurate. Correct answers are $10, answers are $1 and dumb looks are free. In general, I would rate MD simulation somewhere between 0 and $2, maybe sometimes $3.
You can understand thermodynamics as the integrating and weighting the frequency of all structure over all time. Of course, we do not have "all time", but you should understand that some reasonable approximation of "all time" is needed to have even a remotely proper representation of the system.
If you are talking about using the thermodynamic integration for quantifying the free energy of binding for protein-ligand complex then yes it can be done using GROMACS, but as sugested by Prof. Wayne K Dawson you have to take care of issues related to sampling, force field parameters, entropic contribution etc., while making sense from the values you get.
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