[gmx-users] Orientation restraints from FTIR
hleonov at cc.huji.ac.il
Sun Jan 20 17:14:53 CET 2008
We are doing FTIR studies in which we measure a tilt angle of a dipole
to the Z axis. Now we would like to perform a simulation with
orientation restraints according to that angle.
To be more specific, how can we perform an orientation restraints of the
angle between vectors A and B, where vector A is a vector between 2
atoms in the system, and B is the z-axis?
In the documentation of orientation restraints there's a possibility to
input an observable in units of Hz (from NMR, see below), but what we
have as input is the angle between the 2 vectors mentioned above. Is
there a simple way to use the orientation restraints with non-NMR data?
As we understand, ai and aj are two atoms which form vector A (in our
example), how can we make our restraint related to the z-axis here, when
there's no observable?
Thanks in advance,
An example of orientation restraints taken from the gromacs manual:
[ orientation restraints ]
; ai aj type exp. label alpha const. obs. weight; Hz nm3 Hz 1/Hz2
31 32 1 1 3 3 6.083 -6.73 1.0
43 44 1 1 4 3 6.083 -7.87 1.0
55 56 1 1 5 3 6.083 -7.13 1.0
65 66 1 1 6 3 6.083 -2.57 1.0
73 74 1 1 7 3 6.083 -2.10 1.0
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