I just did trjconv with `-pbc nojump` and now the RMSD looks right. I would never expected that. It works!
My 2+ ion is using parameters for nonbonded model without charge transfer found in this paper: J Chem Theory Comput. 2013 June 11; 9(6): 2733–2748. doi:10.1021/ct400146w. This may be useful for people doing runs with metallic nonbonded 2+ ions. *https://docs.google.com/spreadsheets/d/1pzBJU5QP5j4XRtEbN4htQ8j8_GU73G3ZYvkG1YZDKWc/edit?usp=sharing <https://docs.google.com/spreadsheets/d/1pzBJU5QP5j4XRtEbN4htQ8j8_GU73G3ZYvkG1YZDKWc/edit?usp=sharing>* Some approaches do a charge correction redistributing it at the ion ligands, but I can't afford it. Journal of Structural Biology 157 (2007) 444–453 I'm worried because my ion has coordination number 4 or 5, probably requiring charge transfer what is beyond my abilities. So i'm accepting suggestions on how to manage my ion. 2016-06-15 12:29 GMT-03:00 Justin Lemkul <jalem...@vt.edu>: > > > On 6/15/16 10:25 AM, Pedro Lacerda wrote: > >> Very thank you, Justin. >> >> So is just the system that is very unstable. >> >> > Not necessarily. Have you tried fitting with trjconv? I haven't gotten a > clear answer on that. Forget VMD centering, gmx rms -nopbc, etc. Have you > used trjconv and gotten a "clean" trajectory with no jumps or broken > molecules? If not, try it. > > Noob questions follows. >> >> But here other similar system where shows what I expect when the molecule >> is across the boundary. This isn't happening in the previous plot. >> >> gmx rms -s md.tpr -f md.xtc -pbc >> http://postimg.org/image/69fafxdx7/ >> >> gmx rms -s md.tpr -f md.xtc -nopbc >> http://postimg.org/image/swujm2th7/ >> >> Another small question, my metallic ion is attached to the protein even if >> i'm using the nonbonded model. So the interaction site is already >> favorable >> even if not bonded. Now I'm doing the bonded model parametrization but >> from >> your experience this has huge impact? Distances and angles will be >> preserved, or I really need to try both models and compare? >> >> > Metal ions are notoriously hard to deal with in an additive > representation, especially if they are 2+ or larger. Check the literature > for similar systems. > > -Justin > > > >> >> >> 2016-06-15 10:54 GMT-03:00 Justin Lemkul <jalem...@vt.edu>: >> >> >>> >>> On 6/15/16 9:49 AM, Pedro Lacerda wrote: >>> >>> PBC is always considered by default at Gromacs analysis tools, and I >>>> recentered following the standard VMD procedure. >>>> Considering the PBC, the animation looks quite right to me. >>>> >>>> >>>> Well, sure - PBC doesn't care about visualization convenience, but the >>> molecule is clearly "broken" across a boundary at t=0 and you get a huge >>> RMSD at this point with respect to whatever your starting conformation >>> (presumably unbroken, and likely centered) is. Thus, the value is >>> "correct" but probably not truly reflective of what the actual values >>> should be. >>> >>> Can a .top file have a molecule where not all atoms are bonded? >>> >>>> >>>> >>>> Of course. >>> >>> -Justin >>> >>> >>> >>> 2016-06-15 10:39 GMT-03:00 Justin Lemkul <jalem...@vt.edu>: >>>> >>>> >>>> >>>>> On 6/15/16 9:35 AM, Pedro Lacerda wrote: >>>>> >>>>> Thank you, >>>>> >>>>>> >>>>>> I never did it before but I'll try it. And at VMD I recentered the >>>>>> molecule. And looks right to you so much deviation even at the >>>>>> begining? >>>>>> Never happened to me! >>>>>> >>>>>> >>>>>> You're calculating the RMSD of a broken molecule; the animation shows >>>>>> >>>>> that >>>>> quite clearly. You shouldn't do that. >>>>> >>>>> One more question. What happens when two molecules are put as one >>>>> molecule >>>>> >>>>> in .top, like a molecule that are two disjoints graphs or two >>>>>> molecules. >>>>>> Seems to work fine. >>>>>> >>>>>> >>>>>> I don't understand what you're asking here. >>>>>> >>>>> >>>>> -Justin >>>>> >>>>> >>>>> >>>>> >>>>> 2016-06-15 10:00 GMT-03:00 Justin Lemkul <jalem...@vt.edu>: >>>>>> >>>>>> >>>>>> >>>>>> On 6/15/16 8:45 AM, Pedro Lacerda wrote: >>>>>>> >>>>>>> Hi list, >>>>>>> >>>>>>> >>>>>>>> RMSD analysis of trajectories differs very much from the intuition >>>>>>>> gained >>>>>>>> with the visual inspection of trajectories. RMSD has almost 4nm >>>>>>>> while >>>>>>>> the >>>>>>>> video seems correct. >>>>>>>> >>>>>>>> I'm using Amber 14ffSB with an metallic nonbonded ion attached on >>>>>>>> it. >>>>>>>> It >>>>>>>> was converted from Amber files using ACPYPE, the initial structure >>>>>>>> seems >>>>>>>> correct and the problem doesn't seems originated in parametrization >>>>>>>> errors. >>>>>>>> >>>>>>>> Please can you point me some directions to debug this defect? I >>>>>>>> guess >>>>>>>> that >>>>>>>> isn't needed but do I need to attach some relevant file? >>>>>>>> >>>>>>>> Look at the picture of the animation and RMSD of the first 2ns >>>>>>>> trajectory: >>>>>>>> >>>>>>>> http://imgur.com/a/bFCr8 >>>>>>>> >>>>>>>> Please wait for full loading the animated gif, the remaining of the >>>>>>>> .xtc >>>>>>>> look like this first 20s of the gif. The RMSD was taken with the >>>>>>>> -nopbc >>>>>>>> option! If taken without -[no]pbc flag the plot breaks like if PBC >>>>>>>> was >>>>>>>> not >>>>>>>> considered. It looks like quite the opposite from the expected, >>>>>>>> right? >>>>>>>> >>>>>>>> I also measured the RMSD using VMD giving the same results. Maybe >>>>>>>> this >>>>>>>> is >>>>>>>> a >>>>>>>> very simple error, what can I doing wrong? >>>>>>>> >>>>>>>> >>>>>>>> Use trjconv to recenter and make your molecules whole. That's >>>>>>>> standard >>>>>>>> >>>>>>>> practice before computing RMSD. I have had mixed results with >>>>>>> -nopbc >>>>>>> and >>>>>>> do not rely on it. >>>>>>> >>>>>>> -Justin >>>>>>> >>>>>>> -- >>>>>>> ================================================== >>>>>>> >>>>>>> Justin A. Lemkul, Ph.D. >>>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>>>>>> >>>>>>> Department of Pharmaceutical Sciences >>>>>>> School of Pharmacy >>>>>>> Health Sciences Facility II, Room 629 >>>>>>> University of Maryland, Baltimore >>>>>>> 20 Penn St. >>>>>>> Baltimore, MD 21201 >>>>>>> >>>>>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>>>>>> http://mackerell.umaryland.edu/~jalemkul >>>>>>> >>>>>>> ================================================== >>>>>>> -- >>>>>>> Gromacs Users mailing list >>>>>>> >>>>>>> * Please search the archive at >>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>>>>> posting! >>>>>>> >>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>>> >>>>>>> * For (un)subscribe requests visit >>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >>>>>>> or >>>>>>> send a mail to gmx-users-requ...@gromacs.org. >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>> ================================================== >>>>> >>>>> Justin A. Lemkul, Ph.D. >>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>>>> >>>>> Department of Pharmaceutical Sciences >>>>> School of Pharmacy >>>>> Health Sciences Facility II, Room 629 >>>>> University of Maryland, Baltimore >>>>> 20 Penn St. >>>>> Baltimore, MD 21201 >>>>> >>>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>>>> http://mackerell.umaryland.edu/~jalemkul >>>>> >>>>> ================================================== >>>>> -- >>>>> Gromacs Users mailing list >>>>> >>>>> * Please search the archive at >>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>>> posting! >>>>> >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>> >>>>> * For (un)subscribe requests visit >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>>> send a mail to gmx-users-requ...@gromacs.org. >>>>> >>>>> >>>>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 629 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>> ================================================== >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >>> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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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