Hi Anthony,
I assume you've seen the -pbc flag of gmx distance; and IIRC there's also some options for that in the selection syntax. I'm not sure that'll do what you want though. If you're going to make a script, have a look at the Python module MDAnalysis, that has some nifty tools. If you strictly use cubic boxes you can take the modulus of the distance you measured --- but that'll bite you at some point in the future. Peter On 19-12-17 07:06, Anthony Nash wrote: > > Just wondering whether anyone has had any luck with a similar problem? If > not, I’ll knock a script together and make it available. I was hoping not to > reinvent the wheel if there was already a way. > > Regards > Anthony > > On 18/12/2017 06:23, "[email protected] on > behalf of Anthony Nash" <[email protected] on > behalf of [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]. >
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