Hi, From its help: "gmx distance calculates distances between pairs of positions as a function of time. Each selection specifies an independent set of distances to calculate. Each selection should consist of pairs of positions, and the distances are computed between positions 1-2, 3-4, etc."
You've got it computing distances within each group, which is why they have little or no variation and have the length of a C-H bond and maybe a C-C bond. Per "gmx help selections examples", you might try something like "gmx distance -select 'com of HYP1 plus com of GLPInt1' -s -n" I'll add an explicit tip to the help text - you're not the first person to assume that giving it two selection groups gets some kind of distance between the groups. Mark On Wed, Dec 20, 2017 at 7:56 PM Anthony Nash <[email protected]> wrote: > 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, "[email protected] > on behalf of Mark Abraham" < > [email protected] on behalf of > [email protected]> 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 < > [email protected]> > 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, " > [email protected] > > on behalf of Mark Abraham" < > > [email protected] on behalf of > > [email protected]> 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 < > [email protected] > > > > > 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 > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > before > > > posting! > > > > > > * Can't post? Read > http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > or > > > send a mail to [email protected]. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to [email protected]. > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > send a mail to [email protected]. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
