On Mon, May 21, 2012 at 3:09 AM, mu xiaojia <[email protected]> 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 <[email protected]> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> >> ==============================**========== >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<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 [email protected]. >> Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
