Re: [gmx-users] g_hbond index
On 12/19/12 9:37 AM, Kavyashree M wrote: Dear users, While using g_hbond, does it make any difference if I give option 18 and 1 or 1 and 18? Order does not matter. I wanted to find the hydrogen bonding of a group of residues with the whole protein so I had an index of this group. When I give the option as 18 (index number) and 1 (whole protein), I get several messages Hm. This isn't the first time I found this donor (...,...) But later it does calculates. does this mean that it is double counting those interactions? What is group 18? Be mindful of the g_hbond requirement that the chosen groups must be completely unique or completely overlapping. -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
Re: [gmx-users] g_hbond index
Sir, I thought that the order should not matter but when I used 18 - 1 and 1 - 18 the graph were slightly off. Group 18 is a set of residues in that protein with some unique property. I wanted to see the variation of Hbond of these residues with the whole protein. so group 18 is a subset of group 1. Thank you Kavya On Wed, Dec 19, 2012 at 10:06 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/19/12 9:37 AM, Kavyashree M wrote: Dear users, While using g_hbond, does it make any difference if I give option 18 and 1 or 1 and 18? Order does not matter. I wanted to find the hydrogen bonding of a group of residues with the whole protein so I had an index of this group. When I give the option as 18 (index number) and 1 (whole protein), I get several messages Hm. This isn't the first time I found this donor (...,...) But later it does calculates. does this mean that it is double counting those interactions? What is group 18? Be mindful of the g_hbond requirement that the chosen groups must be completely unique or completely overlapping. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] g_hbond index
On 12/19/12 11:43 AM, Kavyashree M wrote: Sir, I thought that the order should not matter but when I used 18 - 1 and 1 - 18 the graph were slightly off. Group 18 is a set of residues in that protein with some unique property. I wanted to see the variation of Hbond of these residues with the whole protein. so group 18 is a subset of group 1. You see a difference likely because you are invoking the command incorrectly (with overlapping index groups) and it is affecting the way the donor and acceptor arrays are constructed. The proper method of analysis is to monitor H-bonds within group 18 and then between group 18 and whatever part of the protein that does not overlap with it. -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
Re: [gmx-users] g_hbond index
Ok thank you. kavya On Wed, Dec 19, 2012 at 10:52 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/19/12 11:43 AM, Kavyashree M wrote: Sir, I thought that the order should not matter but when I used 18 - 1 and 1 - 18 the graph were slightly off. Group 18 is a set of residues in that protein with some unique property. I wanted to see the variation of Hbond of these residues with the whole protein. so group 18 is a subset of group 1. You see a difference likely because you are invoking the command incorrectly (with overlapping index groups) and it is affecting the way the donor and acceptor arrays are constructed. The proper method of analysis is to monitor H-bonds within group 18 and then between group 18 and whatever part of the protein that does not overlap with it. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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
