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].
