[gmx-users] gmx distance
shrinath.kumar at ucdconnect.ie
Mon Jul 23 20:34:09 CEST 2018
Take a look at
to learn about the selection syntax in gromacs. There is an example in the
examples section that does precisely what you want.
"com of group 1 plus com of group 2"
This can be used with gmx distance to compute the distance between these
On 23 July 2018 at 16:32, Mateusz Bieniek <bieniekmat at gmail.com> wrote:
> Hi Andrew,
> I cannot answer your question about gmx distance but I have been using the
> MDAnalysis package for this kind of analysis. I am writing this in case you
> are proficient in python and need more flexibility. The code more or less
> would look like this:
> u=MDAnalysis.Universe(gro, xtc)
> g1 = u.select_atoms('...')
> g2 = u.select_atoms('...')
> for ts in u.trajectory:
> print (g1.center_of_mass(), g2.center_of_mass())
> Best, Mat
> On Mon, Jul 23, 2018 at 4:04 PM Andrew Bostick <andrew.bostick1 at gmail.com>
> > Hi,
> > I want to calculate distance between com of 2 groups (3 and 8)
> > gmx_mpi distance -f md.xtc -s md.tpr -n index.ndx -oav dist.xvg
> > After that:
> > Available static index groups:
> > Group 0 "System" (27599 atoms)
> > Group 1 "Other" (716 atoms)
> > Group 2 "MMM" (704 atoms)
> > Group 3 "LIG" (12 atoms)
> > Group 4 "Water" (26883 atoms)
> > Group 5 "SOL" (26883 atoms)
> > Group 6 "non-Water" (716 atoms)
> > Group 7 "MMM_LIG" (716 atoms)
> > Group 8 "MMM_com" (44 atoms)
> > Specify any number of selections for option 'select'
> > (Position pairs to calculate distances for):
> > (one per line, <enter> for status/groups, 'help' for help, Ctrl-D to end)
> > > ^C
> > How to use option -select?
> > Please guide me to use -select.
> > Thanks
> > AB
> > --
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