Data associated with Estimation of Protein Melting Temperatures Using Small-Ladder Replica Exchange Simulations

Dried trajectory files The trajectory files included are thermodynamically continuous i.e. contain demuxed TREMD trajectories. Each frame of the TREMD trajectories corresponds to 0.1 ns of simulation time. Reference structures (prefix ref_) and their corresponding topology files ('chignolin' in the name) have been included as is. The topology files for the MD simulations have been included in FF14SB/MD_Extras/. It should be noted that the misfolded reference structure has hydrogen atoms while the folded reference does not (use topology files accordingly). This does not affect the results presented since only heavy protein atoms were included in the RMSD calculation step. Updated: Includes dried trajectories of the large ladder (16 replica) simulations with the FF99SB force field. The corresponding input files (topology, input, groupfile, slurm script, restart files) are provided in MD_Extras_FF99SB. Notes for TREMD simulations Files for TREMD simulations have been provided in TREMD/SETUP/ . There, note that NM, NF, NU_ should be set to the number of misfolded, folded and unfolded replicas to be used for initialization. The structure files for these three possible starting configurations have also been provided in TREMD/SETUP/ . As specified above, for 16-replica FF99SB simulations, the relevant simulation files may be found in MD_Extras_FF99SB.tar.gz . Notes for MCMC simulations The MCMC/ directory contains parallel tempering MCMC trajectories and beta values for demultiplexing trajectories. There are 8 setups with 5 repetitions each. Sample input files and an executable have also been included (pg[0-6] and 1dmcmc_).