[gmx-users] Measuring distance to the nearest image

[Anthony Nash]

Hi Alexandr,

Those were my thoughts also. I was just hoping there was something out there already written to save me time. 
Thanks
Anthony


Dr Anthony Nash
BSc (Hons) MSc MSc PhD MRSC 
Department of Physiology, Anatomy & Genetics 
Oxford University
OX1 3PT UK

On 19/12/2017 10:18, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Alexandr Nasedkin" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of nasedkin at chalmers.se> wrote:

    Hi Anthony,
    
    
    Would it work if you take x/y/z components of the distance and subtract 
    ones extending the size of the box in the corresponding direction?
    
    You will need to extract box size from the *.edr file (unless box is of 
    fixed size), further use flag -oxyz from gmx distance for xyz distance 
    components.
    
    
    -Alexandr
    
    
    
    On 19/12/2017 11:05, Peter Kroon wrote:
    > 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, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Anthony Nash" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of 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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