Re: [gmx-users] Peptide distance matrix
On 4/15/13 9:59 AM, Steven Neumann wrote: Dear Gmx Users, I want to calculate a distance matrix of each amino acid (1, 2, ...25) averaged over simulation time with all amino acids. So matrix of 25x25: 1) is there a tool which can do this or just the use of g_dist fof 600 (25x25 - 25) times? 2) Would you recommend any nice visualisation tool (bioinformatic software) to obtain colorful matrix? g_mdmat does all of this. -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] Peptide distance matrix
On Mon, Apr 15, 2013 at 3:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 9:59 AM, Steven Neumann wrote: Dear Gmx Users, I want to calculate a distance matrix of each amino acid (1, 2, ...25) averaged over simulation time with all amino acids. So matrix of 25x25: 1) is there a tool which can do this or just the use of g_dist fof 600 (25x25 - 25) times? 2) Would you recommend any nice visualisation tool (bioinformatic software) to obtain colorful matrix? g_mdmat does all of this. -Justin Thank you. As far as I see it does minimum dostance matrix and I wish to have all distances averaged over the simulation time. Any advices? Steven -- 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
Re: [gmx-users] Peptide distance matrix
On 4/15/13 10:06 AM, Steven Neumann wrote: On Mon, Apr 15, 2013 at 3:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 9:59 AM, Steven Neumann wrote: Dear Gmx Users, I want to calculate a distance matrix of each amino acid (1, 2, ...25) averaged over simulation time with all amino acids. So matrix of 25x25: 1) is there a tool which can do this or just the use of g_dist fof 600 (25x25 - 25) times? 2) Would you recommend any nice visualisation tool (bioinformatic software) to obtain colorful matrix? g_mdmat does all of this. -Justin Thank you. As far as I see it does minimum dostance matrix and I wish to have all distances averaged over the simulation time. Any advices? So you want a per-atom matrix rather than a per-residue matrix? I suspect some quick hacking of g_mdmat would do that, but I don't know of any tool that does so out of the box (nor would your original approach with g_dist, since it works on residue COM, not per-atom, unless you make groups for every single atom). -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] Peptide distance matrix
On Mon, Apr 15, 2013 at 3:55 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 10:06 AM, Steven Neumann wrote: On Mon, Apr 15, 2013 at 3:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 9:59 AM, Steven Neumann wrote: Dear Gmx Users, I want to calculate a distance matrix of each amino acid (1, 2, ...25) averaged over simulation time with all amino acids. So matrix of 25x25: 1) is there a tool which can do this or just the use of g_dist fof 600 (25x25 - 25) times? 2) Would you recommend any nice visualisation tool (bioinformatic software) to obtain colorful matrix? g_mdmat does all of this. -Justin Thank you. As far as I see it does minimum dostance matrix and I wish to have all distances averaged over the simulation time. Any advices? So you want a per-atom matrix rather than a per-residue matrix? I suspect some quick hacking of g_mdmat would do that, but I don't know of any tool that does so out of the box (nor would your original approach with g_dist, since it works on residue COM, not per-atom, unless you make groups for every single atom). -Justin Thanks. I wish to have a distance matrix over the simulation time per-central carbon atom of each residue. shall I specify one index group with all central carbon atoms or 25 different index groups each with Calpa? Steven -- 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
Re: [gmx-users] Peptide distance matrix
And another question: I want to analyze all 5 nanoseconds every 20 ns of my trajectory. Would you suggest using trjcat to create one trajectory first and then process to g_mdmat or can I specify time periods (frames) I wish to analyze? Steven On Mon, Apr 15, 2013 at 4:08 PM, Steven Neumann s.neuman...@gmail.com wrote: On Mon, Apr 15, 2013 at 3:55 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 10:06 AM, Steven Neumann wrote: On Mon, Apr 15, 2013 at 3:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 9:59 AM, Steven Neumann wrote: Dear Gmx Users, I want to calculate a distance matrix of each amino acid (1, 2, ...25) averaged over simulation time with all amino acids. So matrix of 25x25: 1) is there a tool which can do this or just the use of g_dist fof 600 (25x25 - 25) times? 2) Would you recommend any nice visualisation tool (bioinformatic software) to obtain colorful matrix? g_mdmat does all of this. -Justin Thank you. As far as I see it does minimum dostance matrix and I wish to have all distances averaged over the simulation time. Any advices? So you want a per-atom matrix rather than a per-residue matrix? I suspect some quick hacking of g_mdmat would do that, but I don't know of any tool that does so out of the box (nor would your original approach with g_dist, since it works on residue COM, not per-atom, unless you make groups for every single atom). -Justin Thanks. I wish to have a distance matrix over the simulation time per-central carbon atom of each residue. shall I specify one index group with all central carbon atoms or 25 different index groups each with Calpa? Steven -- 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
Re: [gmx-users] Peptide distance matrix
On 4/15/13 11:17 AM, Steven Neumann wrote: And another question: I want to analyze all 5 nanoseconds every 20 ns of my trajectory. Would you suggest using trjcat to create one trajectory first and then process to g_mdmat or can I specify time periods (frames) I wish to analyze? You have to concatenate whatever intervals you want. Each command only takes one -b and -e flag, not multiple intervals. -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] Peptide distance matrix
On 4/15/13 11:08 AM, Steven Neumann wrote: On Mon, Apr 15, 2013 at 3:55 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 10:06 AM, Steven Neumann wrote: On Mon, Apr 15, 2013 at 3:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 9:59 AM, Steven Neumann wrote: Dear Gmx Users, I want to calculate a distance matrix of each amino acid (1, 2, ...25) averaged over simulation time with all amino acids. So matrix of 25x25: 1) is there a tool which can do this or just the use of g_dist fof 600 (25x25 - 25) times? 2) Would you recommend any nice visualisation tool (bioinformatic software) to obtain colorful matrix? g_mdmat does all of this. -Justin Thank you. As far as I see it does minimum dostance matrix and I wish to have all distances averaged over the simulation time. Any advices? So you want a per-atom matrix rather than a per-residue matrix? I suspect some quick hacking of g_mdmat would do that, but I don't know of any tool that does so out of the box (nor would your original approach with g_dist, since it works on residue COM, not per-atom, unless you make groups for every single atom). -Justin Thanks. I wish to have a distance matrix over the simulation time per-central carbon atom of each residue. shall I specify one index group with all central carbon atoms or 25 different index groups each with Calpa? All C-alpha carbons are in a default index group. Choose it when prompted by g_mdmat and you'll get what you want. -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] Peptide distance matrix
Thank you for this. Steven On Mon, Apr 15, 2013 at 4:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 11:08 AM, Steven Neumann wrote: On Mon, Apr 15, 2013 at 3:55 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 10:06 AM, Steven Neumann wrote: On Mon, Apr 15, 2013 at 3:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 9:59 AM, Steven Neumann wrote: Dear Gmx Users, I want to calculate a distance matrix of each amino acid (1, 2, ...25) averaged over simulation time with all amino acids. So matrix of 25x25: 1) is there a tool which can do this or just the use of g_dist fof 600 (25x25 - 25) times? 2) Would you recommend any nice visualisation tool (bioinformatic software) to obtain colorful matrix? g_mdmat does all of this. -Justin Thank you. As far as I see it does minimum dostance matrix and I wish to have all distances averaged over the simulation time. Any advices? So you want a per-atom matrix rather than a per-residue matrix? I suspect some quick hacking of g_mdmat would do that, but I don't know of any tool that does so out of the box (nor would your original approach with g_dist, since it works on residue COM, not per-atom, unless you make groups for every single atom). -Justin Thanks. I wish to have a distance matrix over the simulation time per-central carbon atom of each residue. shall I specify one index group with all central carbon atoms or 25 different index groups each with Calpa? All C-alpha carbons are in a default index group. Choose it when prompted by g_mdmat and you'll get what you want. -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
Re: [gmx-users] Peptide distance matrix
And last question: Are these minimum distances averaged over the simulation time? Cannot find any equation the way it is calculated... in Manual its written: This minimum distance between two residues Ai and Aj is defined as the smallest distance between any pair of atoms (i 2 Ai, j 2 Aj ). The output is a symmetrical matrix of smallest distances between all residues. And nothing else... Steven On Mon, Apr 15, 2013 at 4:24 PM, Steven Neumann s.neuman...@gmail.comwrote: Thank you for this. Steven On Mon, Apr 15, 2013 at 4:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 11:08 AM, Steven Neumann wrote: On Mon, Apr 15, 2013 at 3:55 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 10:06 AM, Steven Neumann wrote: On Mon, Apr 15, 2013 at 3:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 9:59 AM, Steven Neumann wrote: Dear Gmx Users, I want to calculate a distance matrix of each amino acid (1, 2, ...25) averaged over simulation time with all amino acids. So matrix of 25x25: 1) is there a tool which can do this or just the use of g_dist fof 600 (25x25 - 25) times? 2) Would you recommend any nice visualisation tool (bioinformatic software) to obtain colorful matrix? g_mdmat does all of this. -Justin Thank you. As far as I see it does minimum dostance matrix and I wish to have all distances averaged over the simulation time. Any advices? So you want a per-atom matrix rather than a per-residue matrix? I suspect some quick hacking of g_mdmat would do that, but I don't know of any tool that does so out of the box (nor would your original approach with g_dist, since it works on residue COM, not per-atom, unless you make groups for every single atom). -Justin Thanks. I wish to have a distance matrix over the simulation time per-central carbon atom of each residue. shall I specify one index group with all central carbon atoms or 25 different index groups each with Calpa? All C-alpha carbons are in a default index group. Choose it when prompted by g_mdmat and you'll get what you want. -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
Re: [gmx-users] Peptide distance matrix
On 4/15/13 12:08 PM, Steven Neumann wrote: And last question: Are these minimum distances averaged over the simulation time? Cannot find any equation the way it is calculated... in Manual its written: This minimum distance between two residues Ai and Aj is defined as the smallest distance between any pair of atoms (i 2 Ai, j 2 Aj ). The output is a symmetrical matrix of smallest distances between all residues. And nothing else... The question is answered by reading g_mdmat -h. -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] Peptide distance matrix
Hey, For the average distance matrix, you can use g_rmsdist. Cheers, Tsjerk On Mon, Apr 15, 2013 at 6:19 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 12:08 PM, Steven Neumann wrote: And last question: Are these minimum distances averaged over the simulation time? Cannot find any equation the way it is calculated... in Manual its written: This minimum distance between two residues Ai and Aj is defined as the smallest distance between any pair of atoms (i 2 Ai, j 2 Aj ). The output is a symmetrical matrix of smallest distances between all residues. And nothing else... The question is answered by reading g_mdmat -h. -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 -- Tsjerk A. Wassenaar, Ph.D. -- 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
