[gmx-users] eigenvalues

sanjay23 at iitb.ac.in sanjay23 at iitb.ac.in
Sat Jan 10 07:34:04 CET 2009

Hi Tsjerk,
actually my protein is quite larg (509 aa).i had divided my trajectory in
different part and according to your suggestion i calculated
cosine-content for all, and find that trajectory from 5to15 ns and
18to25ns having cosine value very less about 0.03 in both cases(with and
without ligands), while other combination showing higher values (>0.6).so
i think my system is Ist converges around 5ns and maintaining it up to 15
ns after that it may be few conformational fluctuation occurring and
finally it get stabilized from 18to15ns.may that part 15to18ns trajectory
is transition period between to conformational fluctuation. i have also
calculated temp. and pressure during whole simulation and i find that it
is exact Gaussian between 5to25ns.so my confusion is whether i take my
trajectory for ED analysis is from 5to15 or 18to25 or whole from 5to25,
but 5to25 showing value of cosine >0.6.

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