Dear users, *When I use g_hbond with -contact and -r 0.4 on C-alpha atoms -* I get the following message - *************************************************************************** Reading frame 0 time 4000.000 Will do grid-seach on 26x26x19 grid, rcut=0.4 Last frame 500 time 5000.000 Found 509 different contacts in trajectory Found 0 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 474/474 - Reduced number of hbonds from 509 to 509 - Reduced number of distances from 0 to 0 Average number of contacts per timeframe 0.000 out of 112338 possible
------------------------------------------------------- Program g_hbond, VERSION 4.5.3 Source code file: gmx_hbond.c, line: 4052 Range checking error: Variable y has value 0. It should have been within [ 0 .. 0 ] For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- *************************************************************************** *With the option -contact -r2 0.4 on C-alpha atoms I get-* **************************************************************************** Reading frame 0 time 4000.000 Will do grid-seach on 26x26x19 grid, rcut=0.4 Last frame 500 time 5000.000 Found 4 different contacts in trajectory Found 507 different atom-pairs within second cut-off distance Merging hbonds with Acceptor and Donor swapped 474/474 - Reduced number of hbonds from 4 to 4 - Reduced number of distances from 507 to 507 *With the option -contact -r 0.35 -r2 0.4 on C-alpha atoms I get-* **************************************************************************** Reading frame 0 time 4000.000 Will do grid-seach on 26x26x19 grid, rcut=0.4 Last frame 500 time 5000.000 Found 4 different contacts in trajectory Found 507 different atom-pairs within second cut-off distance Merging hbonds with Acceptor and Donor swapped 474/474 - Reduced number of hbonds from 4 to 4 - Reduced number of distances from 507 to 507 The index and the matrix that it writes has only 4 contacts (highlighted). Why is it says as Hbond? But isnt the "507" the number of contacts? What is the 4 hbonds? What do I need to do If I want to get the C-alpha contacts in the form of a matrix, which gives the presence/absence of a contact over the entire simulation? Kindly help.. Thank you Kavya On Tue, Feb 19, 2013 at 9:56 AM, Kavyashree M <[email protected]> wrote: > 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 <[email protected]> wrote: > >> Hello Sir, >> >> I used C-alpha atoms. >> >> Kavya >> >> >> On Mon, Feb 18, 2013 at 11:28 PM, Erik Marklund <[email protected]>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 <[email protected]> >>>> wrote: >>>> >>>> Thank you! >>>>> >>>>> >>>>> On Thu, Feb 14, 2013 at 3:38 PM, Erik Marklund <[email protected] >>>>> >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 [email protected] >>>>>>> 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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