Beg your pardon, I have not ignored your comment entirely regarding using specific residue COM. I just recently succeeded performing md_umbrella simulation (using protein COM) on few configurations. . I have not used specific residues COM so far as because of some confusions regrading defining it. The residue stretch is not continuous e.g. residue 6-10, 78-80, 56, 63, 35 are to be active site residue. I got no idea how to define such discrete set of residues using make_ndx command.
On Sun, May 21, 2017 at 8:13 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/21/17 9:47 AM, abhisek Mondal wrote: > >> I did try the code successfully on a configuration generated after >> pulling. >> The NVT approach with direction-periodic geometry worked nicely for the >> particular configuration. >> >> However, when I tried to reapply the same code (with modified COMs and >> thus >> pull_vec) on a different configuration, something awkward happened. The >> ligand got pulled through protein and got stuck inside it. I have put the >> trajectory movie alongwith md_umbrella.mdp file here: >> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0 >> >> Would you please care to give some advise regarding this odd behavior. >> >> > Likely some elements of your setup are inadequate. You have a large, > flexible ligand, so perhaps using its overall COM is inappropriate. You're > also using the entire protein COM as the other end of the reaction > coordinate, and perhaps that's not good enough (I've suggested a number of > times to be judicious in the choice of residues taken as the group > corresponding to the protein, but it seems you're simply not doing that so > I'll stop suggesting it). Perhaps your pull vector is calculated > incorrectly. A lot going on. Back up and do something simpler, a test > case that is easy to define so you can get comfortable with setting these > things up and understanding/diagnosing weird behavior. > > -Justin > > > Thank you. >> >> On Fri, May 19, 2017 at 5:18 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 5/19/17 5:56 AM, abhisek Mondal wrote: >>> >>> On Thu, May 18, 2017 at 6:48 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>>> >>>> >>>> >>>>> On 5/17/17 8:55 AM, abhisek Mondal wrote: >>>>> >>>>> This time I think I got ligand restrained successfully during the >>>>> >>>>>> umbrella >>>>>> sampling. I have removed the restrain from protein, as per your >>>>>> advice. >>>>>> Defined the COM vector in md_umbrella.mdp, applied pull_k1=1000 and >>>>>> used >>>>>> pull_rate1=0.0. >>>>>> I have uploaded the trajectory movie (and other mdp files) in the >>>>>> following >>>>>> link: >>>>>> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0 >>>>>> >>>>>> However, I'm facing a problem. Due to the withdrawal of the position >>>>>> restrain of protein. The protein and ligand (together) is moving >>>>>> around >>>>>> the >>>>>> box and resulting in "Distance of pull group 1 (10.441990 nm) is >>>>>> larger >>>>>> than 0.49 times the box size (10.646989)" error. >>>>>> >>>>>> As per the video I have uploaded, if I assume this approach worked, >>>>>> then >>>>>> how can I avoid this error ? Is there any way to make sure the >>>>>> protein-ligand remains in the middle of the box (or nearby). I have >>>>>> taken >>>>>> pretty large box compared to the protein structure from the beginning. >>>>>> >>>>>> Please suggest me a way out. >>>>>> >>>>>> >>>>>> Use a larger box or use direction-periodic geometry. >>>>>> >>>>> >>>>> >>>> >>>> For the sake of computational power I'm leaning towards >>>> direction-periodic >>>> geometry. However, from the mailing list entries I found out that >>>> pressure >>>> coupling should not be used for this kind of geometry setup. >>>> NVT coupling with no velocity generation is what I'm opting for. There >>>> are >>>> a lot of doubt regarding the md_umbrella.mdp setup using NVT protocol. >>>> Would you please suggest if the code ( >>>> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0) >>>> looks >>>> sensible ? >>>> >>>> Eagerly waiting for your opinion. >>>> >>>> >>>> Try it and see what happens. >>> >>> -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. > -- Abhisek Mondal *Senior Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA* -- 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.