Sir, I tried -nomerge. It is fine now. But will it be wrong to calculate without nomerge option?
Thank you Kavya On Fri, Mar 22, 2013 at 9:28 PM, Erik Marklund <er...@xray.bmc.uu.se> wrote: > I could see how -merge (on by default) could lead to this. Have you tried > -nomerge? > > Erik > > > On Mar 22, 2013, at 4:46 PM, Kavyashree M wrote: > > Dear Users, >> >> As suggested earlier by Erik I used 4.6 to calculate the hydrogen bonds. >> Still the >> Total intra-protein hydrogen bonds is not equal (MM +MS +SS) hydrogen >> bond. >> Is there any other solution? >> >> Thank you >> Kavya >> >> On Fri, Jan 25, 2013 at 4:11 PM, Kavyashree M <hmkv...@gmail.com> wrote: >> >> Dear Sir, >>> >>> Sure I will try with 4.6. presently I am not able to download it. >>> >>> Thank you >>> kavya >>> >>> >>> On Fri, Jan 25, 2013 at 4:04 PM, Erik Marklund <er...@xray.bmc.uu.se >>> >wrote: >>> >>> There were a handful of bugfixes to g_hbond over the last year. Could >>>> you >>>> try 4.6 or a smoking hot 4.5.5? I recognize this discrepancy form >>>> before. >>>> >>>> Erik >>>> >>>> >>>> On Jan 24, 2013, at 3:59 PM, Kavyashree M wrote: >>>> >>>> Dear Sir, >>>> >>>>> >>>>> This is 4.5.3. I have not tried nomerge. I did not use >>>>> nomerge option in any of them, So if it has counted >>>>> it (Hbond b/w same donor and acceptor but with >>>>> different hydrogen) twice in one calculation then it will >>>>> be counted twice in another, So wont the result with/without >>>>> nomerge be the same? >>>>> >>>>> The difference is 4-5 Hbonds.. >>>>> >>>>> Thank you >>>>> Kavya >>>>> >>>>> On Thu, Jan 24, 2013 at 7:30 PM, Erik Marklund <er...@xray.bmc.uu.se> >>>>> wrote: >>>>> >>>>> Hi. What version was this? Have you tried with -nomerge? >>>>> >>>>>> >>>>>> Erik >>>>>> >>>>>> >>>>>> On Jan 21, 2013, at 10:55 AM, Kavyashree M wrote: >>>>>> >>>>>> Dear users, >>>>>> >>>>>> >>>>>>> While calculating hydrogen bonds for a simulation, it >>>>>>> was found that the average number of intra protein >>>>>>> hbonds was not equal to sum of MM, MS and SS >>>>>>> hydrogen bonds. (MM - main chain - main chain, >>>>>>> MS - main chain - side chain and side chain - side >>>>>>> chain hydrogen bonds). There was a difference of 5 >>>>>>> or so hbonds between intra-protein and MM+MS+SS >>>>>>> hbonds. why is this so? >>>>>>> I selected the options 7 7 for MM, 7 8 for MS and 8 8 >>>>>>> for SS hydrogen bonds. >>>>>>> >>>>>>> One clarification. nhbdist option gives 0, 1, 2, 3 and >>>>>>> total hydrogen bonds per hydrogen. Does this mean >>>>>>> that a single hydrogen involving in forming hbond with >>>>>>> 2 different acceptors/donors at different points of time >>>>>>> in the trajectory. >>>>>>> >>>>>>> Thanks >>>>>>> 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> >>>>>>> > >>>>>>> <htt**p://lists.gromacs.org/**mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/**listinfo/gmx-users> >>>>>>> <h**ttp://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/**<http://www.gromacs.org/Support/**> >>>>>>> >>>>>>> Mailing_Lists/Search<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. 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