[gmx-users] Measuring distance to the nearest image
Anthony Nash
anthony.nash at dpag.ox.ac.uk
Wed Dec 20 09:55:47 CET 2017
Hi Mark,
I think with a combined project list as long as my arm and going between VMD and Gromacs that the fault lies with me. A misunderstanding with the decimal point. However, I am a little confused over the output and despite reading the help I am still none the wiser.
I go on to select two groups:
[ HYP1 ] ← part of the side chain of a hydroxyproline
4669 4670 4672 4673 4676 4677
[ GLPInt1 ] ←
563 564 566 567 570 571 574 576
I assume the average absolute distance between the two groups will be the same regardless of which one you take your measurement (as x1, y1, z1) from. My output looks like:
@ title "Average distance"
@ xaxis label "Time (ps)"
@ yaxis label "Distance (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "HYP1"
@ s1 legend "GLPInt1"
10000.000 0.109 0.159
10000.200 0.109 0.159
10000.400 0.109 0.160
Reflected in the on-screen output (I have just used a tiny sample size to run this very quickly, the standard deviation in the larger sample size is much different)
Analyzed 501 frames, last time 100.200
HYP1:
Number of samples: 1503
Average distance: 0.10900 nm
Standard deviation: 0.00000 nm
GLPInt1:
Number of samples: 2004
Average distance: 0.15911 nm
Standard deviation: 0.05431 nm
I want the distance between HYP1 and GLPInt1. Why the two measurements? Clearly there is something I do not understand about the gmx distance command.
Really hope you can clear this up. Thanks again!
Anthony
On 19/12/2017 11:25, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Mark Abraham" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of mark.j.abraham at gmail.com> wrote:
Hi,
An example where the structure comes from a single frame would be a useful
thing to explore whether the code is working correctly. I don't think the
composition of the index groups should matter, but I can't see how the code
wouldn't work correctly.
Mark
On Tue, Dec 19, 2017, 10:12 PM Anthony Nash <anthony.nash at dpag.ox.ac.uk>
wrote:
> Hi Mark,
>
> As an example, from numerous attempts, I have tried:
>
> /usr/local/gromacs5.1.2/bin/gmx_d distance -pbc -b 10000 -f
> crosslinked_0_20.trr -s crosslinked_0_20.tpr -n index.ndx
>
> which was throwing a value of around 8 nm, rather than the 2 nm I was
> expecting if it took a measurement from over the periodic boundary.
>
> Unfortunately, I’ve left the necessary harddrive at home. I’’’ be more
> than happy to respond with a more comprehensive example along with output
> data in a few hours.
>
> Thanks
> Anthony
>
>
> On 19/12/2017 11:02, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> on behalf of Mark Abraham" <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
> mark.j.abraham at gmail.com> wrote:
>
> Hi
>
> This is exactly what two well chosen selections should produce, given
> a tpr
> and the PBC option. What have you tried that didn't work as you
> expected?
>
> Mark
>
> On Mon, Dec 18, 2017, 5:23 PM Anthony Nash <anthony.nash at dpag.ox.ac.uk
> >
> wrote:
>
> >
> > Hi all,
> >
> > I am trying to measure the distance between the COM of two side chain
> > functional groups across the periodic boundary to their nearest image
> > rather than across the unit cell itself. I have tried several gromacs
> > distance commands with no success and more at random as I trawl
> through the
> > help and manual, so I won’t replicate those commands here.
> >
> > This link is a hand drawn image of what I am trying to do. I would
> like to
> > measure how far apart the two large dots are across the periodic
> boundary.
> > VMD gives me roughly 1 nm, but the Gromacs commands give me 8 nm as
> it
> > takes the measurement from within the unit cell.
> >
> >
> >
> https://www.researchgate.net/profile/Anthony_Nash3/post/How_to_calculate_distance_between_groups_into_the_nearest_image_using_Gromacs/attachment/5a30d10eb53d2f0bba43e5c3/AS:571001131417600@1513148686095/image/IMG_20171213_065534.jpg
> > If this involve a tcl script in VMD I would appreciate knowing how
> to code
> > for an atom selection in a “Periodic” image rather than the “Self”.
> >
> > Loads of thanks!
> > Anthony
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