Table 2Description of various molecular dynamics methods: characteristics, limits and applications
Linear timedependance?
Reactioncoordinatedependance?
Methods to biasthe system
Characteristics
Limits
Examples of application
cMD
Yes
No
No bias introduced
Need long simulation time to cross high
energy barrier
l
Conformational sampling
l
Study of Binding/unbinding process
l
Characterization of open/close state of protein stateand opening/closingchannels
Scaled MD
&aMD
Modification
of potentialenergysurface
l
Sampling is not directed
l
Add of a modified potential energyto the original potential energy
Long simulations often lead to greater
statistical errors
l
Conformational sampling
l
Characterization of open/close state of protein stateand opening/closingchannels
l
Estimation of free energy
US & SMD
Yes
l
Sampling along a geometricalreaction coordinate (distance,angle, etc)
l
Add an harmonic potential energyto the original potential energy
l
Choice of reaction coordinate
l
Bias parametrization is very systemdependent
l
Conformational sampling
l
Study of Binding/unbinding process
l
Study of unfolding/foldingprocess
l
Characterization of open/close state of protein andopening/closing channels
l
Estimation of free energy ofstudied events
TMD
l
Sampling along the RMSD asreaction coordinate
l
Add an harmonic potential energyto the original potential energy
MTD
l
Sampling along collective variablesdefined as one or a combination ofgeometrical reaction coordinate
l
Add a Gaussian potential energy tothe original potential energy
Choice of CVs
REMD
No
No
Multicopy
searchingandsampling
l
Sampling is not directed
l
Several variants of REMD: T-REMD, R-REMD, H-REMD, M-REMD etc.
l
No time evolution of structuralevents
l
Number of replicas dependent onsize system
Conformational sampling
SA
Temperature
scaling
l
Sampling is not directed
l
Sampling equivalent to the unbiasedsystem
No time evolution of structural events
410 Sonia Ziada et al.