21 maj 2012 kl. 06.54 skrev Anirban: > > > 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
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 <[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 > > ======================================== > -- > 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 > > -- > 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 ----------------------------------------------- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 [email protected] http://www2.icm.uu.se/molbio/elflab/index.html
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