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. 2018 Sep 6;13(9):e0202764. doi: 10.1371/journal.pone.0202764

Fig 5. Validation of temperature coupling schemes for Trp-cage.

Fig 5

The width of the kinetic energy distributions sampled by the different schemes differ significantly when the solute is coupled to a separate thermostat. The data is reported numerically in Table G in S3 Text. This plot lists the temperature equivalent (see Eq 12) of the mean and the variance of the internal temperature of the Trp-cage peptide for nine different thermostat coupling schemes. All coupling schemes keep the average temperature close to its target value of 300K. When using a single thermostat to couple the entire system, the width of the distribution is very close to the expected value for all thermostats. When coupling the solute to a separate thermostat, the VR algorithm samples the expected distribution. The WC algorithm is found to sample a distribution which is clearly too narrow, while the NH thermostat samples a slightly too wide distribution. When coupling only the solvent to a heat bath, small deviations of low statistical significance can be observed in all cases.