From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Tue Mar 10 2015 - 06:19:16 CDT
Dear Users,
I am now trying to harmonically restraint a dihedral angle of four
selections of atoms using colvar for a regular NPT simulation. However the
colvar manual does not give clearly how it defined the dihedral angle from
the 4 groups.
For example, referring to figure 3 at wiki (
http://en.wikipedia.org/wiki/Dihedral_angle), does a sequence - group 1 2 3
4 means that group 2 and 3 are overlapped and angle between b1(1-2) and
b2(4-3) is measured?
Also, how actually does the colvar treat a selection of atom when
calculating the distances or angles? Is it using the center of mass or
center of geometry?
Thanks in advance,
Kevin
City University of Hong Kong
This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:20:57 CST