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Bug #309

g_msd fitting arguments: odd behaviour

Added by Jussi Lehtola over 10 years ago. Updated over 10 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Erik Lindahl
Category:
analysis tools
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

Hi,

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.

History

#1 Updated by Berk Hess over 10 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.

Berk

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