On 5/11/17 1:25 PM, abhisek Mondal wrote:
Alright. I'm trying as per your advice. Actually my system is pretty big and due to constraint of computation power it is taking me more time to test vector setup. I really appreciate your time. Thanks a lot for your suggestions. One thing I'm worried about here. In previous mail, I mentioned the "distance at start" and "ref at t=0" is negative. What does the negative value signify, I mean how can distance be negative ? Is is due to my poorly given vector definition or something else ?
It's a vector quantity. It can be positive or negative depending on how you define the groups and what their positions are. And you're telling grompp to pull along the negative-z dimension.
-Justin
On Thu, May 11, 2017 at 9:03 PM, Justin Lemkul <jalem...@vt.edu> wrote:On 5/11/17 9:21 AM, abhisek Mondal wrote: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 -1Note that with "direction" geometry, only pull_vec1 is acting. pull_dim is ignored. The ligand was previously moving along x,y direction when I was usingpull_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.Again you're trying to just apply the restraint to one dimension and it looks to be fairly arbitrary. I already suggested using the vector connecting the ligand COM with the binding site residues' COM and using that as pull_vec1. Draw it out. It makes a lot more sense than trying to restrain only along one axis, which as I have said before, makes no sense in this case. -JustinI 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 onlyalong 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 andy 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 besuitably 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 sphericalsymmetry, 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 ornot 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 giveme 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 thetutorial, 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? 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-- ================================================== 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.
