[gmx-users] interpolating frames between extremes

[Dave M]

Hi All,

I have a question/confusion regarding interpolate frames option '-nframes'
in gmx anaeig.

One can find the extreme conformations as dot products projected on a
selected eigenvector (to simplify say first eigenvector PC1). As the manual
says, with -nframes (in anaeig) one can interpolate between the two
extremes. I am confused with 'interpolating' here:
a) Are these interpolated frames, between extremes, the 'real'
conformations extracted from the trajectory? Which in that case one cannot
define nframes > total frames falling between the extremes (dot product
projections min and max on selected eigenvector). I don't think am right
here because I could simply use a filtering option in anaeig.
Or
b) Are these interpolated smoothened frames some kind of predicted
conformations along a path? In that case these interpolated conformations
cannot be considered as 'real' conformational changes (that is they are not
extracted from the trajectory) occurring between the extremes. Many times
people show beautiful animations (interpolations between extremes), then
they are not true conformational changes extracted from the trajectory. In
that case I should not trust their visual explanations about the
conformational changes. But I believe, please correct me, the interpolation
is done using some intermediate real frames extracted from the trajectory
otherwise it will not look so smooth.

I hope I was able to ask my source of confusion clearly.

Thanks
Dave