On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal <abhisek.m...@gmail.com> wrote:
> Hi, > > Thank you for the explanation. It really cleared some concepts. But I'm > still having my ligand moving in this step. I have modified the code as: > ; Pull code > pull = umbrella > pull_ngroups = 1 > pull_group0 = Protein_chain_A > pull_group1 = ACO > pull_geometry = direction ; simple distance increase > pull_dim = Y Y Y ; not to allow ligand move along other > dir > pull_rate1 = 0.0 > pull_k1 = 1000 ; kJ mol^-1 nm^-2 > pull_start = yes ; define initial COM distance > 0 > pull_vec1 = 0 0 -1 > > The ligand was previously moving along x,y direction when I was using > pull_dim = N N Y. So I changed it to Y in all direction and provided 0 as > vector and pull_rate1=0.0, so that it does not move much. But at the end > of a 10ns run, I see that the ligand is still moving as it was earlier. > It shows me: Pull group natoms pbc atom distance at start reference at t=0 0 1132 936665 1 59 1618 -1.555 -1.555 Is it ok withe negative value ? Anyway this setup is not working. > > I have choose my reaction coordinate to be along -Z axis and want to apply > biasing potential accordingly with restraining the ligand movement. Can you > please suggest where am I failing with this code ? > > Thank you. > > > > On Tue, May 9, 2017 at 1:11 AM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 5/8/17 10:00 AM, abhisek Mondal wrote: >> >>> On Sun, May 7, 2017 at 11:37 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>>> >>>> On 5/7/17 1:57 AM, abhisek Mondal wrote: >>>> >>>> Hi, >>>>> >>>>> For your ease of understanding regarding what is happening during this >>>>> above said umbrella-mdrun, I have shared the trajectory video file the >>>>> following link. >>>>> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0 >>>>> >>>>> Is this normal given that the mdp code being used ? I basically have no >>>>> idea with this step, so please help me out. I'm using gromacs-4.6.2. >>>>> >>>>> >>>>> Your setup is incorrect. You're applying a biasing potential only >>>> along >>>> z, so the ligand can move freely along x and y. A protein-ligand >>>> complex >>>> has spherical symmetry, so you should set the reaction coordinate to the >>>> vector connecting the ligand with some suitable subset of interacting >>>> protein residues. >>>> >>> >>> >>> I don't get it. >>> We are trying not to move our configuration (generated after pulling >>> simulation) along the reaction coordinate, so for restraining we are >>> supposed to set pull_rate1=0.0. >>> >> >> Of course. But you said set pull_k = 0 which does not make sense. The >> pulling rate *is* zero during umbrella sampling (no net displacement, >> restrain to the specified distance along the reaction coordinate) and >> pulling force constant should be non-zero. >> >> If applying biasing potential only along z is causing movement along x and >>> y then what if we apply the biasing potential along x,y,z ? Will it cause >>> any good in restraining the ligand? >>> >>> >> This is how it should be done. The reaction coordinate should be >> suitably defined based on the geometry of the system. As I suggested >> before, choose some representative residues in the active site as one group >> and the ligand as the other. Thus defines the reaction coordinate without >> any presupposition of anything being aligned with a Cartesian axis, which >> is rarely the case. >> >> Moreover, you said previously "A protein-ligand complex has spherical >>> symmetry, so you should set the reaction coordinate to the vector >>> connecting the ligand with some suitable subset of interacting protein >>> residues.". It is really unclear to me, could you please give me some >>> examples to understand it more simply? I had pulled the ligand along -z >>> axis, doesn't it mean that the reaction coordinate is to be that way ? >>> The >>> fact that I'm struggling with is to restrain the pull configurations for >>> further sampling. >>> >>> >> The reaction coordinate is whatever you define it to be. Whether or not >> pulling along the z-axis makes sense depends on the orientation of the >> system and the intrinsic geometry. In your case, it doesn't make sense. >> In my case (the tutorial, the unidirectional growth of an amyloid fibril) >> it does make sense to use a single Cartesian axis for the SMD portion and >> subsequent umbrella sampling. >> >> I'm really a beginner, so maybe I'm asking stupid questions. Please give >>> me >>> some advise. I'm really unable to decipher the scenario in comparison to >>> your amyloid article in JPCB. >>> >>> >> You should read the article to understand why I did what I did in the >> tutorial, and then move on to reading articles that are more similar to >> your case. These will be much more relevant to what you're doing. >> >> -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. >> > > > > -- > Abhisek Mondal > > *Senior Research Fellow* > > *Structural Biology and Bioinformatics Division* > *CSIR-Indian Institute of Chemical Biology* > > *Kolkata 700032* > > *INDIA* > -- 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.