Is it possible to correlate stability difference between different peptides by doing unfolding MD simulation at 400K?
Yes, it is possible by doing unfolding MD simulation. You can actually calculate the lifetime of a peptide in particular conformer and you can comment on its stability with other peptides. Infact, the more time protein takes to unfold, the more stable it is in that particular conformation.
I would like to add that we have a pretty rough force fields. In some cases, proteins may be stable at 400K.
I would wondered what happens to water above 373K. Especially, in regard to the correct parameterization of the available water models. So I searched for information and found this discucion: http://lists.gromacs.org/pipermail/gmx-users/2003-March/004557.html
and moreover, this interesting work: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2480669/
which somehow validates your question, at least with the SPC water model.
You can also consider steered MD simulations, by computing PMF may be more effective to predict the stability in your case.
If the molecules of interest are small peptides (say, up to ~12 residues), it is realistically feasible to perform proper folding simulations using replica exchange or adaptive tempering in explicit solvent and with full (PME-based) electrostatics which will allow you to explicitly determine thermal stability. For such small peptides (and corresponding small -in terms of number of atoms- systems) you can do something like ~50 nanosecond per day on a single quad-core machine with a fat NVIDIA card using NAMD, or even more with GROMACS. This translates to ~40 days of compute time (per node) for ~2 μs of simulation time -which for small peptides may be adequate for mapping their folding landscape as a function of temperature (using for example, Q vs. T diagrams).
My twocents.
Another way to analyze unfolded peptide dynamics applying molecular dynamics was discussed at http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0032131 and http://dx.doi.org/10.1126/science.1208351
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