Re: [gmx-users] Distance calculation
g_mindist also has something useful in this direction, I guess. Dr. Vitaly V. Chaban On Sat, Sep 14, 2013 at 12:10 AM, Rama ramkishn...@gmail.com wrote: Hi , I there any tool to calculate distance between particular atom from one group(protein) to particular atom from another group(DMPC lipid in Bilayer). For Example: protein backbone Amide(HN) to acyl chain carbon atom(C2D) in DMPC lipid. Thanks Rama -- View this message in context: http://gromacs.5086.x6.nabble.com/Distance-calculation-tp5011170.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-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 listgmx-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] Distance calculation
Hi , I there any tool to calculate distance between particular atom from one group(protein) to particular atom from another group(DMPC lipid in Bilayer). For Example: protein backbone Amide(HN) to acyl chain carbon atom(C2D) in DMPC lipid. Thanks Rama -- View this message in context: http://gromacs.5086.x6.nabble.com/Distance-calculation-tp5011170.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-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
Re: [gmx-users] distance calculation
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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] distance calculation
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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] distance calculation
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 listgmx-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 listgmx-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 listgmx-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 listgmx-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] distance calculation
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 ? -- Tarak -- gmx-users mailing listgmx-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
Re: [gmx-users] distance calculation
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. 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 listgmx-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 listgmx-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
Re: [gmx-users] distance calculation
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 listgmx-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 listgmx-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
