Dihedral definition in NAMD

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,

City University of Hong Kong

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