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> >>>> > >>>> * 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. Use the >>>> www interface or send it to gmx-users-requ...@gromacs.org. >>>> * Can't post? 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