# Re: Spinangle with refgroup : Warning: discontinuous rotation!

From: nicolas martin (nicolasmartin973_at_gmail.com)
Date: Wed Apr 09 2014 - 10:41:35 CDT

Dear all,

I have made some interesting statements. Using 3 dummyAtoms placed on the
very position of the carbons C1 C2 and C3 of my butane molecule, and
restraining the distance between each carbon and its dummyAtom. This was
done in order to have an absolute restrain on those 3 atoms, I mean not
even diffusion because if I'm right the RMSD restrain of those 3 atoms
would have led to a rigid body able to diffuse.
Since I had 3 atoms under an absolute restrain I decided to remove the
reference groupand calculate the spinangle of the last carbon (C4 and its
H) along the rotation axis defined as the bon C2-C3. Once again if I'm not
making any mistakes this should similar as computing the dihedral angle
C1-C2-C3-C4.

What is interesting is when I use a center and a target in the input file
bellow you can see an example, the spinangle colvar is going from 0 to 180
more or less smoothly according to the forceConstant that I chose but I
definitely can see an evolution from a point A to a point B. BUT, because
there must be one, if I visualize the simulation in VMD and plot this
dihedral angle, I can clearly see that the butane is behaving like if there
was no restrain... I can see it jumping from 60 to 180 with are two minima
for this dihedral angle.

How can I be sure then that using the spinangle here could be correlated to
what I wanna see which is a spinning of the extracellular domain of a
receptor around the axis going through it and while the transmembrane
domain remain fixed.

NM

colvarsTrajFrequency 100
#colvarsRestartFrequency 20000
colvarsTrajAppend on

colvar {
name d1
distance {
group1 { atomnumbers 1 }
group2 { dummyatom (3.367 , 4.696 , -0.124) }
}
}
colvar {
name d5
distance {
group1 { atomnumbers 5 }
group2 { dummyAtom (3.590 , 6.009 , 0.659) }
}
}
colvar {
name d8
distance {
group1 { atomnumbers 8 }
group2 { dummyAtom (4.998 , 6.546 , 0.976) }
}
}
colvar {
name d6 # d6 and d7 are the two H on C2 that I use
distance {
group1 { atomnumbers 6 }
group2 { dummyAtom (2.933 , 5.801 , 1.530) }
}
}
colvar {
name d7
distance {
group1 { atomnumbers 7 }
group2 { dummyAtom (3.134 , 6.752 , -0.030) }
}
}

harmonic {
name dummies
colvars d1 d5 d8 d6 d7
centers 0 0 0 0 0
forceConstant 1000
}

colvar {
name spinangle
spinangle {
axis (-1.408,-0.537,-0.317) # axe de la liaison C2 C3

atoms {atomNumbers 11 12 13 14 #..moving group
}
refPositionsFile input/buta.pdb

}
}
harmonic {
name harmonic
colvars spinangle
forceConstant 0.006
centers 0
targetCenters 180
targetNumSteps 1000
targetNumStages 19

2014-04-07 18:33 GMT+02:00 nicolas martin <nicolasmartin973_at_gmail.com>:

> Dear NAMD users,
>
> As part of my project, I planned to compute the spinangle of the upper
> part of the protein and set the lower part as a reference. To develop my
> method i chose to work with deca-alanine working with one extremity,
> computing the spinangle of the last part of ALA10 around an axis, defined
> as the axis going through one bound nearby. This spinangle is then
> restrained to obtain a rotation of the mobile part of my selection. Exactly
> as one would do computing a dihedral angle and restraining it to explore
> [-180;180[.
>
> I tried to be as clear as possible to explain what I aim to do, but I am
> sure that is no trivial thing to get. Anyway my point by seeking for help
> is that I cannot success in running long simulations of this system. For
> the short ones, I got some "Warning: discontinuous rotation!" but the
> simulation can end properly. When I try to elongate the simulation, the
> velocities of random atoms happens to be too high so does the temperature
> of the system and the calculation crash before term.
>
> I figured out by deduction that this "discontinuous rotation" was due to a
> bestfit step (which could occur in both spinangle and refgroup) but since I
> do not really understand why I might be mistaken. Maybe this is the way I
> want to restrain and compute this spinangle which is totally wrong. You
> will find below the definition of my colvar.
>
> Hoping you can help me on this one, bests,
>
> Nicolas Martin
> Laboratoire d'Ingenierie des Fonctions Moleculaires
> Universite de Strasbourg
>
> colvar {
> name spinangle
> spinangle {
> atoms {
> atomNumbers 92 93 94 95 96 99 100 101 102 103 104 # measure group
> centerReference on
> rotateReference on
> refPositionsGroup { # reference group
> atomNumbersRange 1-91
> }
> refPositionsFile input/ref.pdb
> refPositionsCol O
> refPositionsColValue 1.00
> }
> refPositionsFile input/mesure.pdb
> refPositionsCol O
> refPositionsColValue 1.00
> axis (-0.476,0.644,1.189) # rotation axis defined along a bond
> }
> }
> harmonic {
> name harmonic
> colvars spinangle
> forceConstant 0.0060923 # this should be equal to 10kcal/mol/radian
> centers -180
> targetCenters 180
> targetNumSteps 50000
> targetNumStages 37
> }
>
> colvar {
> name rmsd
> rmsd {
> atoms { atomNumbersRange 1-91 # reference part is restrained by RMSD
> }
> refPositionsFile input/ref.pdb
> }
> }
> harmonic {
> colvars rmsd
> forceConstant 3000
> centers 0
> }
>
>

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