[gmx-users] AFM: .pdo output format

[mon_sharma at research.iiit.ac.in]

Dear All,

I am using pull code to perform AFM on some protein. My pull 
dimensions are pulldim as Y Y Y for x,y and z coordinates. the output .pdo 
files are generated, and as far as I have understood, it 
will get the .pdo output as:
time (t), position of ref group (xr,yr,zr), position of pulled 
group(xp,yp,zp) and position of spring (xs,ys,zs)
and accordingly, I am getting 10 columns output:
t xr yr zr xp yp zp xs ys zs

In the manual it is written that "position of pulled group and spring are 
in absolute coordinates. Subtract the reference coordinate to get the 
position relative to the pulled group."

which I suppose means that the extension (difference between the pulled 
group and reference group) should be like =
dist=sqrt( (xr-xp)2 + (yr-yp)2 + (zr-zp)2 )

But when I am calculating this way, I am getting very less 
distance values, which otherwise, when i am doing geometry calculations, 
they are coming quite higher. I am quite confused. I think I am missing something 
very important which I am not able to make out. If anyone can please help 
me out....

Thanks a lot in advance,
Regards,
Monika Sharma