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)
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 -- Tarak -- 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
