VMD-L Mailing List

From: Himanshu Khandelia (hkhandel_at_memphys.sdu.dk)
Date: Fri Jan 19 2007 - 05:41:31 CST

Hi,

I am trying to rotate the principal axis of one molecule in my system to
align with the z axis. I use the following, as earlier suggested in the
mailing list:

##############
# if $vec is the principal vector
set M [transvecinv $vec]
$sel move $M
set M [transaxis y -90]
$sel move $M
###############

However, my molecule is not located at the origin, and hence the rotation
(which is around the origin, probably) also results in overall
translation. Is there a straightforward way to prevent overall translation
while trying to implement rotations in NAMD ?

Thank you,

-Himanshu