From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Nov 24 2014 - 08:46:48 CST
Hi JC,
I'm still not sure what's happening in your case. Another way to
investigate, if you use the development version of VMD, is to compute the
colvar on-the-fly in there. E.g. you can load your trajectory and issue
these commands:
cv molid top
cv configfile myconfig.in # wherein you could define both the tilt and
orientation
then:
cv frame <n>
cv update
cv printframe # will print values of all currently defined colvars
That way you can inspect your trajectory interactively. You can also move
the helix manually and calculate the new colvar value, to check that it
matches your intuition.
I hope that helps.
Jerome
PS: command "cv" might actually be "colvars" depending on exactly which
development version you have.
On 22 November 2014 at 15:10, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> Here’s the entire file. In TMorientrev.ref, the helix is aligned with the
> z-axis.
>
>
> Colvarstrajfrequency 20
> ##Colvarsrestartfrequency 100
>
> colvar {
> name position
>
> width 0.5
>
> distanceZ {
> forceNoPBC yes
> main {
> atomnumbers { 7 9 24 25 26 28 43 44 45 47 62 63 64 66 81 82 83 85
> 100 101 102 104 119 120 121 123 138 139 140 141 145 147 }
> }
> ref {
> atomnumbers { 168 220 272 324 376 428 480 532 584 636 688 740 792
> 844 896 948 1000 1052 1104 1156 1208 1260 1312 1364 1416 1468 1520 1572
> 1624 1676 1728 1780 1832 1884 1936 1988 2040 2092 2144 2196 2248 2300 2352
> 2404 2456 2508 2560 2612 2664 2716 2768 2820 2872 2924 2976 3028 3080
> 3132 3184 3236 3288 3340 3392 3444 3496 3548 3600 3652 3704 3756 3808 3860
> 3912 3964 4016 4068 4120 4172 4224 4276 4328 4380 4432 4484 4536 4588
> 4640 4692 4744 4796 4848 4900 4952 5004 5056 5108 5160 5212 5264 5316 5368
> 5420 5472 5524 5576 }
> }
> }
> }
>
> colvar {
> name tilt
>
> width 0.05
>
> tilt {
> atoms {
> atomnumbers { 7 9 24 25 26 28 43 44 45 47 62 63 64 66 81 82 83 85
> 100 101 102 104 119 120 121 123 138 139 140 141 145 147 }
> }
> refPositionsFile {
> input/TMorientrev.ref
> }
> refPositionsCol { O }
> }
> }
>
> # P atoms
> colvar {
> name Pin
>
> width 1.0
>
> lowerboundary -5.0
> upperboundary 5.0
>
> lowerwallconstant 50.0
> upperwallconstant 50.0
>
> distanceZ {
> main {
> atomnumbers { 168 220 272 324 376 428 480 532 584 636 688 740 792
> 844 896 948 1000 1052 1104 1156 1208 1260 1312 1364 1416 1468 1520 1572
> 1624 1676 1728 1780 1832 1884 1936 1988 2040 2092 2144 2196 2248 2300 2352
> 2404 2456 2508 2560 2612 2664 2716 2768 2820 2872 2924 2976 3028 3080
> 3132 3184 3236 3288 3340 3392 3444 3496 3548 3600 3652 3704 3756 3808 3860
> 3912 3964 4016 4068 4120 4172 4224 4276 4328 4380 4432 4484 4536 4588
> 4640 4692 4744 4796 4848 4900 4952 5004 5056 5108 5160 5212 5264 5316 5368
> 5420 5472 5524 5576 }
> }
> ref {
> dummyatom ( 0.0, 0.0, 0.0 )
> }
> }
> }
>
> harmonic {
> name tiltpos
> colvars tilt position
> centers 0.0 0.0
> forceConstant 1.0
> }
>
>
>
>
> On Nov 22, 2014, at 7:00 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
>
> > Hi JC,
> >
> > Can you post the config for your tilt colvar?
> >
> > Jerome
> >
> > On 22 November 2014 at 01:12, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> >
> >> I tried your idea of replacing tilt with orientation. For an example
> >> frame, I get for the quaternion (0.31, 0.37, 0.59, -0.64). I then
> loaded
> >> this frame along with my reference frame, translated both so that they
> were
> >> centered on the origin, and then, using quaternion2rmatrix.tcl, applied
> a
> >> rotation. It went from something like this
> >>
> >> | /
> >> | /
> >> | /
> >> | /
> >>
> >> to this
> >>
> >> |
> >> |
> >> |
> >> | ———— (a bit misleading, it’s not perfectly aligned with any axis, but
> is
> >> certainly more planar)
> >>
> >> Clearly it doesn’t agree with the expected rotation. Comparing the
> >> matrices
> >>
> >> q2r
> >> -0.52 0.83 -0.11
> >> 0.04 -0.10 -0.98
> >> -0.84 -0.53 0.02
> >>
> >> and measure fit from VMD gives
> >> -0.35 -0.85 -0.39
> >> 0.81 -0.48 0.33
> >> -0.47 -0.20 0.86
> >>
> >> Shouldn’t these give the same values? What’s going on here?
> >>
> >> Thanks,
> >> JC
> >>
> >> On Nov 21, 2014, at 12:35 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> >> wrote:
> >>
> >> Hi JC, one issue could be that the helix changes structure internally,
> and
> >> the rigid-body assumption breaks down, but perhaps you checked already
> for
> >> that.
> >>
> >> Another possibility is that the axis is not what it's supposed to be,
> i.e
>
>
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