Dear Apramita, Right. Still, the same still applies with regards to the -666.
It could be a matter of statistics, why you get sensible values for the longer trajectory chunk. Also, note that the trajectory length limits the possible timescales that the model can tease out. If I understand correctly, your trajectories with and without pic have different length, so I’m not surprised that the kinetic constants that you get out are different. Kind regards, Erik ______________________________________________ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 29 Aug 2017, at 14:02, Apramita Chand <apramita.ch...@gmail.com<mailto:apramita.ch...@gmail.com>> wrote: Dear Eric, Its actually the DG(kj/mol) value which is -666. The time is coming to be-126 ps. But the g_hbond is failing to fit the kinetic model to the data for the last 60ns as you have implied. Any reasons why this could have happened, while for the entire trajectory, I am getting positive values? But for the entire trajectory, with and without pbc(1793ps and 2345ps respectively) , I have two separate values for lifetime. Which one should I take? I would be appreciative of any suggestions Looking forward to your help, yours sincerely Apramita *Message:( 2 Date: Tue, 29 Aug 2017 08:09:32 +0000 From: Erik Marklund <erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> <erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>>> To: "gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org> <gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org>>" <gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org> <gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org>>> Subject: Re: [gmx-users] Difference in Hydrogen Bond Lifetimes on truncating trajectory and also on using pbc Message-ID: <e2a33c50-036b-4dc7-9f79-bc136147f...@kemi.uu.se<mailto:e2a33c50-036b-4dc7-9f79-bc136147f...@kemi.uu.se> <e2a33c50-036b-4dc7-9f79-bc136147f...@kemi.uu.se<mailto:e2a33c50-036b-4dc7-9f79-bc136147f...@kemi.uu.se>>> Content-Type: text/plain; charset="utf-8" Dear Apramita, IIRC, the time is set to.-666 when gmx hbond fails to fit the kinetic model to the data. Not the most informative way of indicating an error perhaps. Kind regards, Erik ______________________________* *________________ Erik Marklund, PhD, Marie Sk?odowska Curie INCA Fellow Department of Chemistry ? BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> <erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>><* *mailto:erik.markl...@kemi.uu.se <erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>>> On 29 Aug 2017, at 07:20, Apramita Chand <apramita.ch...@gmail.com<mailto:apramita.ch...@gmail.com> <apramita.ch...@gmail.com<mailto:apramita.ch...@gmail.com>><* *mailto:apramita.ch...@gmail.com <apramita.ch...@gmail.com<mailto:apramita.ch...@gmail.com>>>> wrote: Dear All, I've carried out a 100ns simulation of protein in water and want to calculate hydrogen bond (forward) lifetime between Protein-Water. Initially, I thought it would be better to analyse hydrogen bonds in last 60ns of simulation, so I truncated the trajectory using g_trjconv using -b 40000 -e 100000 as options. The results came as *ACF 10628/10628Normalization for c(t) = 0.0621737 for gh(t) = 2.07246e-06Back Off! I just backed up hbac1.xvg to ./#hbac1.xvg.1#Hydrogen bond thermodynamics at T = 300 KFitting parameters chi^2 = 2.8733Q = 0-----------------------------* *---------------------Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2Forward -0.008 -126.851 -666.000 2.8733* (This came for both with and without pbc). I also tried to do it from the g_hbond command itself by giving starting time as 40ns and ending as 100ns, but again it came negative lifetime. Next, I tried g_trjconv with application of -pbc mol -ur compact options on untruncated(100ns) trajectory. The results came as: *ACF 11303/11303Normalization for c(t) = 0.0615891 for gh(t) = 1.23179e-06Back Off! I just backed up hbac1.xvg to ./#hbac1.xvg.2#Hydrogen bond thermodynamics at T = 300 KFitting parameters chi^2 = 3.03095Q = 0-----------------------------* *---------------------Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2Forward 0.001 1793.775 23.259 3.03095* When I tried the same with the original unconverted trajectory(without g_trjconv ,without pbc options), I got a lifetime of *2345.890ps*. *My question is ,1) why do the truncated trajectories give negative values for my simulation?* *2)If I take the whole 100ns for analysis of hydrogen bond lifetime, which value should I take, since application of pbc gives a different value than that of the original trajectory value of lifetime.* I would be very grateful for your help. Looking forward to your suggestions Yours sincerely Apramita Chand* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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