In a paper I have read the term GMEC, which was not further explained. GMEC stands for Global Minimum Energy Conformation. But what is it? Is it just the conformation with the lowest energy?
Yes. It is the conformer with the lowest energy out of all possible conformers.
There are also local minima which have a lower energy than conformations either side of the them on the energy diagram but do not have the lowest possible energy.
In this diagram showing the conformers of butane we can see that all three stable conformers; the two gauche conformers and the anti conformer are at local energy minima but the anti conformer is the global minimum.
GMEC is typically used within the GMEC-model, a model within the protein design field that entails the following. The backbone of the protein is not allowed to move, the interaction energies between atoms are pairwise additive, the amino acid side chains are allowed to change only between discrete states, c.q. rotamers, and the goal is to compute the GMEC and its corresponding amino acid sequence.
So depending on the context where you came across this ambiguous term, it may carry more assumptions than would be clear at first sight.