Table 4.
Experiment | MD | REMD | ||||||
---|---|---|---|---|---|---|---|---|
RNase- variant |
pH | peak [cm−1] |
FWHM [cm−1] |
peak [cm−1] |
FWHMb [cm−1] |
peak [cm−1] |
FWHMb [cm−1] |
Null shiftc [cm−1] |
SCN | 4.5 | 2154.4 | 9.0 | 2154.8 | 4.5 | 2155.3 | 5.4 | 2162.0 |
8.0 | 2156.2 | 10 | 2157.5 | 4.9 | 2157.5 | 6.3 | ||
pCN | 4.5 | 2231.2 | 5.9 | 2234.4 | 3.1 | 2233.4 | 4.2 | 2233.2 |
8.0 | 2231.5 | 5.7 | 2232.5 | 2.8 | 2232.7 | 3.1 | ||
mCN | 4.5 | 2233.9 | 10 | 2230.8a | 7.8 a | 2232.0a | 7.8 a | 2233.8 |
α only | 2234.4 | 8.2 | 2233.4 | 8.9 | ||||
β only | 2230.3 | 5.6 | 2231.5 | 6.1 | ||||
8.0 | 2233.4 | 10 | 2232.5a | 6.6 a | 2232.9a | 7.3 a | ||
α only | 2233.7 | 8.0 | 2233.2 | 8.5 | ||||
β only | 2232.2 | 4.9 | 2232.9 | 5.6 | ||||
avg. error |
0.3 | 0.5 | 2.9 | |||||
RMS error |
2.0 | 1.5 | 4.1 |
Calculated from a concatenated trajectory from both α and β conformers.
FWHM approximated as for a Gaussian distribution as where σ is the variance of the distribution of frequencies.
The null shift equals the reference frequency used and provides a comparison of how well the simulation does relative to no electrostatic perturbation.