Hi Tsjerk, i used the command in format-
g_mindist -f md.xtc -s md.tpr -n 13.ndx -od 13.xvg -on 13.xvg -o 13.out -b 500 -e 1500 -d 0.5 so here i obtain the output- atmpair.out- 0.000000e+00 13 21161 1.000000e+00 13 21161 2.000000e+00 13 21161 3.000000e+00 13 21161 4.000000e+00 13 21161 5.000000e+00 13 21161 6.000000e+00 13 21161 7.000000e+00 13 21161 8.000000e+00 13 21161 9.000000e+00 13 21161 1.000000e+01 13 21161 1.100000e+01 13 21161 1.200000e+01 13 21161 1.300000e+01 13 21161 1.400000e+01 13 21161 1.500000e+01 13 18698 1.600000e+01 13 21161 1.700000e+01 13 18698 1.800000e+01 13 18698 1.900000e+01 13 18698 2.000000e+01 13 18698 2.100000e+01 13 21455 2.200000e+01 13 7142 2.300000e+01 13 7142 and distance output- 0.000000e+00 1.360443e+00 1.000000e+00 1.246777e+00 2.000000e+00 1.386871e+00 3.000000e+00 1.250959e+00 4.000000e+00 1.314306e+00 5.000000e+00 1.273990e+00 6.000000e+00 1.175991e+00 7.000000e+00 1.154678e+00 8.000000e+00 1.249905e+00 9.000000e+00 1.110049e+00 1.000000e+01 1.023204e+00 1.100000e+01 1.004968e+00 1.200000e+01 1.214452e+00 1.300000e+01 1.297469e+00 1.400000e+01 1.307791e+00 1.500000e+01 1.276168e+00 1.600000e+01 1.552775e+00 1.700000e+01 1.668275e+00 1.800000e+01 1.786125e+00 1.900000e+01 1.733398e+00 2.000000e+01 1.656987e+00 2.100000e+01 1.715875e+00 2.200000e+01 1.848419e+00 2.300000e+01 1.932844e+00 Now my doubt is the whether these distances shown are the exact distance ie actual or the minimum distance measured between the two atoms. Thanks On Thu, Sep 22, 2011 at 12:13 PM, Tsjerk Wassenaar <tsje...@gmail.com>wrote: > Hi Aiswarya, > > What did you do, what did you get, what did you expect and what is > your hunch regarding the difference between your result and your > expectation? > > Tsjerk > > On Thu, Sep 22, 2011 at 8:21 AM, aiswarya pawar > <aiswarya.pa...@gmail.com> wrote: > > Hi users, > > > > The g_mindist gives the minimum distance between the atoms other than the > > actual distance. > > > > Thanks > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > * Groningen Institute for Biomolecular Research and Biotechnology > * Zernike Institute for Advanced Materials > University of Groningen > The Netherlands > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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