g_msd fitting arguments: odd behaviour
at least in gromacs 4.0.4 the arguments and output of g_msd seem to be in conflict.
The program accepts on top of the normal arguments -b and -e arguments for the time period used to fit the diffusion constant, -beginfit and -endfit.
It is quite unclear to me what is the origin of -beginfit and -endfit (is t(begin of fitting) = t(begin) + t(beginfit) [or t(begin of fitting) = t(beginfit)]). Also the output doesn't have any mention of the real time coordinates of the trajectory file used.
#1 Updated by Berk Hess almost 12 years ago
There is not conflict.
MSD is not a function of the simulation time,
but of the time difference used for the analysis.
-beginfit and -endfit work on t of MSD, not on the trajectory.
MSD is determined using many different starting points
along the trajectory.