[gmx-users] Measuring distance to the nearest image
anthony.nash at dpag.ox.ac.uk
Tue Dec 19 12:03:29 CET 2017
Those were my thoughts also. I was just hoping there was something out there already written to save me time.
Dr Anthony Nash
BSc (Hons) MSc MSc PhD MRSC
Department of Physiology, Anatomy & Genetics
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:
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
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.
> 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.
>> 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.
>> 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!
>> 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 gmx-users-request at gromacs.org.
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 gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users