thanks a lot Mark On Thu, Sep 20, 2012 at 12:31 PM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > On 20/09/2012 4:21 PM, tarak karmakar wrote: >> >> Thanks Mark. >> I was using the following command as I got it in the manual. >> g_dist -f traj.xtc -s topol.tpr -n index.ndx -o dist.xvg >> But I could not able to find the way how to specify the indices of the >> two desired atoms. >> ( suppose I want to plot the distance between atom no. 500 (protein >> backbone) and atom no. 879 (ligand atom) with respect to time) > > > See manual 8.1 for discussion, and > http://www.gromacs.org/Documentation/Gromacs_Utilities/make_ndx for more. > > > Mark > >> On Thu, Sep 20, 2012 at 10:20 AM, Mark Abraham <mark.abra...@anu.edu.au> >> wrote: >>> >>> On 20/09/2012 2:05 PM, tarak karmakar wrote: >>>> >>>> Thanks Justin. >>>> >>>> But in my case I want to plot the distance between one atom in the >>>> backbone of the protein and other atom present in the ligand. Then how >>>> can I specify these two atoms I need for plotting the distance between >>>> them. >>> >>> >>> g_dist treats the system as a list of atoms, and is ignorant of details >>> like >>> molecules. So you just need to tell it which atoms via their indices. >>> >>> Mark >>> >>> >>>> On Thu, Sep 20, 2012 at 12:26 AM, Justin Lemkul <jalem...@vt.edu> wrote: >>>>> >>>>> >>>>> On 9/19/12 2:55 PM, tarak karmakar wrote: >>>>>> >>>>>> Dear All, >>>>>> >>>>>> I want to calculate the distance between the nitrogen atom present in >>>>>> the ligand and the H- attached to the backbone of the protein along a >>>>>> long trajectory. So can anyone suggest me how to consider these two >>>>>> atoms to calculate and plot the distance along with the time ? >>>>>> >>>>> g_dist with appropriate index groups. >>>>> >>>>> -Justin >>>>> >>>>> -- >>>>> ======================================== >>>>> >>>>> Justin A. Lemkul, Ph.D. >>>>> Research Scientist >>>>> Department of Biochemistry >>>>> Virginia Tech >>>>> Blacksburg, VA >>>>> jalemkul[at]vt.edu | (540) 231-9080 >>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>>>> >>>>> ======================================== >>>>> -- >>>>> 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 >>>> >>>> >>>> >>> -- >>> 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 >> >> >> > > -- > 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
-- Tarak Karmakar Molecular Simulation Lab. Chemistry and Physics of Materials Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P. O. Bangalore - 560 064 Karnataka, INDIA Ph. (lab) : +91-80-22082809 -- 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