1LVZ is an analog of the C-terminal undecapeptide of the α-subunit of the heterotrimeric G protein transducin, check the paper "Structure and Orientation of a G Protein Fragment in the Receptor Bound State from Residual Dipolar Couplings".
Replica Exchange Simulation were performed in vacuum, gb implicit and explict solvent. 32 replicas 1000 exchanges.
following are the movies of the three simulations:
The acceptance rate for vacuum is ~65%, implicit ~63%, explicit ~1%.
following are simulation from random structures.
To create trajectories for explicit solvent, we need to change the trajarchive2dcd.pl, mark off rexanalysis.pl, and use readArchive.pl, because if we use rexanalysis,pl. the number of atoms in trajectory does not agree with number of atoms in final.pdb of that replica, It will take much longer time, but I really don't know how to work around this.