Re: [gmx-users] intermolecular H bond selection
21 maj 2012 kl. 06.54 skrev Anirban: On Mon, May 21, 2012 at 3:09 AM, mu xiaojia muxiaojia2...@gmail.com wrote: Thanks for prompt answering but I may need to clarify my question and sorry for the understanding, For example, I have dipeptides like Ala-Ala, how to ask g_hbond only calculate the h bonds between Ala on different dipeptides instead of counting all the possible h bonds between Ala(intermolecularly and intramolecularly) Make two groups with make_ndx that contains the residue numbers (or specific atom numbers) of the ALA residues between which you want to count the H bonds and then select these group numbers with g_hbond. -Anirban And if you have many alanines you might have to call g_hbond many times (think in the lines of scripting). Or invoke g_hbond once with the index group consisting of all alanines chosen twice and decompose the hbonding matrix (-hbm -hbn) yourself (python/perl). Best, Erik Thanks very much! On Fri, May 18, 2012 at 7:57 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 5/18/12 7:22 PM, mu xiaojia wrote: Hi gmx-users, I have a question might be explained before but I cannot understand from the previous , how to calculation the intermolecular h-bonds between two molecules? I saw someone mentioned using a second tpr file, but how to do it specifically? Thanks very much! g_hbond asks for two index groups to be selected. Assign each molecule to an index group and select them when prompted. -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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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] intermolecular H bond selection
Thanks for prompt answering but I may need to clarify my question and sorry for the understanding, For example, I have dipeptides like Ala-Ala, how to ask g_hbond only calculate the h bonds between Ala on different dipeptides instead of counting all the possible h bonds between Ala(intermolecularly and intramolecularly) Thanks very much! On Fri, May 18, 2012 at 7:57 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 5/18/12 7:22 PM, mu xiaojia wrote: Hi gmx-users, I have a question might be explained before but I cannot understand from the previous , how to calculation the intermolecular h-bonds between two molecules? I saw someone mentioned using a second tpr file, but how to do it specifically? Thanks very much! g_hbond asks for two index groups to be selected. Assign each molecule to an index group and select them when prompted. -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] intermolecular H bond selection
On Mon, May 21, 2012 at 3:09 AM, mu xiaojia muxiaojia2...@gmail.com wrote: Thanks for prompt answering but I may need to clarify my question and sorry for the understanding, For example, I have dipeptides like Ala-Ala, how to ask g_hbond only calculate the h bonds between Ala on different dipeptides instead of counting all the possible h bonds between Ala(intermolecularly and intramolecularly) Make two groups with make_ndx that contains the residue numbers (or specific atom numbers) of the ALA residues between which you want to count the H bonds and then select these group numbers with g_hbond. -Anirban Thanks very much! On Fri, May 18, 2012 at 7:57 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 5/18/12 7:22 PM, mu xiaojia wrote: Hi gmx-users, I have a question might be explained before but I cannot understand from the previous , how to calculation the intermolecular h-bonds between two molecules? I saw someone mentioned using a second tpr file, but how to do it specifically? Thanks very much! g_hbond asks for two index groups to be selected. Assign each molecule to an index group and select them when prompted. -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 -- 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] intermolecular H bond selection
Hi gmx-users, I have a question might be explained before but I cannot understand from the previous , how to calculation the intermolecular h-bonds between two molecules? I saw someone mentioned using a second tpr file, but how to do it specifically? Thanks very much! Ja -- 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] intermolecular H bond selection
On 5/18/12 7:22 PM, mu xiaojia wrote: Hi gmx-users, I have a question might be explained before but I cannot understand from the previous , how to calculation the intermolecular h-bonds between two molecules? I saw someone mentioned using a second tpr file, but how to do it specifically? Thanks very much! g_hbond asks for two index groups to be selected. Assign each molecule to an index group and select them when prompted. -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
