[gmx-users] ED analysis, domain rotation, DynDom

jo hanna jfhanna at gmail.com
Fri Mar 7 23:50:20 CET 2008


I have a done number of MD simulations of a two domain protein with
different ligands and also in the apo state. Comparing these simulations I
see varying degrees of domain rotation of the one domain relative to the
other which I want to quantitatively measure and I was thinking of using
DynDom to do this; I have already assessed a number of structures taken from
different points throughout the simulations but want a to assess the motion
throughout the simulations.
>From the user lists I read that I should do ED analysis first. Is this using
g_covar and then g_anaeig or using make_edi and then doing ED in mdrun and
then assessing these results?
Also as the motion appears to be the C-terminal domain relative to the
N-terminal domain when using g_covar should I fit over the N-terminal domain
backbone but do the analysis over the whole backbone, or just fit over the
whole backbone? Also in g_covar is it better for this type of problem to use
the -ref option and assess the deviation from the conformation in the
structure file instead of from the average?
I would appreciate some guidance as although I've read some papers on this
subject I am a bit confused as to what is the best way to progress.

Many thanks,

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