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
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
