From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Nov 24 2014 - 14:42:43 CST
Thanks - I was meaning to look into this option. I figured it out. It’s the wrapping, or lack there of. When the protein is split across the boundary, I get the value from the simulation. When I use PBC tools to join the fragment, it gives the value I expect. I really didn’t expect this behavior at all.
Is the solution to turn off wrapAll? Restrain the protein to the box center?
Thanks,
JC
On Nov 24, 2014, at 9:46 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
> 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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