Sir, My purpose was to compare two simulations of the same protein at different temperatures. So I wanted to see how the interaction of each residue with other residues, within a cut-off, varies between the two. by using the matrix of C-alpha contact over the whole trajectory.
Thank you kavya On Tue, Feb 19, 2013 at 9:50 AM, Kavyashree M <hmkv...@gmail.com> wrote: > Hello Sir, > > I used C-alpha atoms. > > Kavya > > > On Mon, Feb 18, 2013 at 11:28 PM, Erik Marklund <er...@xray.bmc.uu.se>wrote: > >> Hi, >> >> With -r2 one can provide a second, larger, cutoff so that contact >> kinetics can be analyzed within the Luzar-Chandler framework that were >> designed for hbonds. >> >> What index groups did you use? >> >> Erik >> >> >> On Feb 18, 2013, at 6:04 PM, Kavyashree M wrote: >> >> Dear users, >>> >>> As Suggested by Erik, I used g_hbond with -contact to obtain a matrix of >>> each contact as a function of time. I used the following command - >>> g_hbond -f a.xtc -s a.tpr -contact -r2 0.5 -hbm m.xpm -b 4000 -e 4400 >>> -hbn >>> c.ndx >>> >>> I get only three contacts in the index file. The protein is a dimer of >>> 474 >>> residues >>> (237 each). With a distance cut off of 0.5nm there should have been more >>> number >>> of contacts. And what is the difference in using -r only or -r2 only and >>> combining -r >>> and -r2? >>> >>> Thank you >>> Kavya >>> >>> On Thu, Feb 14, 2013 at 3:40 PM, Kavyashree M <hmkv...@gmail.com> wrote: >>> >>> Thank you! >>>> >>>> >>>> On Thu, Feb 14, 2013 at 3:38 PM, Erik Marklund <er...@xray.bmc.uu.se >>>> >wrote: >>>> >>>> Perhaps g_hbond -contact will do what you want. >>>>> >>>>> Erik >>>>> >>>>> >>>>> On Feb 14, 2013, at 10:42 AM, Kavyashree M wrote: >>>>> >>>>> Dear users, >>>>> >>>>>> >>>>>> How can I get the number of interactions of each residue >>>>>> within a cut off as a function of time. just like g_saltbr writes >>>>>> with the option -sep. >>>>>> I tried using g_mdmat but it gives an average contact map. >>>>>> >>>>>> Thank you >>>>>> Kavya >>>>>> -- gmx-users mailing list gmx-users@gromacs.org >>>>>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>>>>> <htt**p://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<h**ttp://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. 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