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/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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