GROMACS Tutorial

Summary

You have now hopefully been successful in conducting umbrella sampling simulations by generating a series of configurations along a reaction coordinate, running biasing simulations, and extracting the PMF. The .mdp files provided here serve as examples only, and should not be considered broadly applicable to all systems. Review the literature and the GROMACS manual for adjustments to these files for efficiency and accuracy purposes.

If you have suggestions for improving this tutorial, if you notice a mistake, or if anything else is unclear, please feel free to email me. Please note: this is not an invitation to email me for GROMACS problems. I do not advertise myself as a private tutor or personal help service. That's what the GROMACS User Forum is for. I may help you there, but only in the context of providing service to the community as a whole, not just the end user.

Happy simulating!

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