It finished normally then. I got another question. I was pulling along XZ plane. Distances I got is not a arithmetic progression with respect to different configurations. I mean the output looks like: 50 1.3637913 51 1.3729873 52 1.4363521 53 1.4652436 54 1.4503893 55 1.4260585 56 1.3836564 57 1.3918289 58 1.3942112 59 1.4296075 60 1.4574580 61 1.3772060 62 1.3604678 63 1.3986934 64 1.3650020 65 1.3965892 66 1.4247549 67 1.4097543 68 1.4460622 69 1.3933917 70 1.4080330 71 1.4576371 72 1.4678355 73 1.4853811 74 1.4144009 75 1.4365107 76 1.4342467 77 1.4353391 78 1.4025292 79 1.4092745 80 1.4392823 81 1.4330521 82 1.4404603 83 1.3839875 84 1.3936158 85 1.3747249 86 1.4166344 87 1.3945516 88 1.3606738 89 1.3709180 90 1.3676665 91 1.3724216 92 1.3779051 93 1.3530073 94 1.3227006 95 1.3054955 96 1.2701077 97 1.3492427 98 1.3388848 99 1.3286418 100 1.3590064 101 1.3886772 102 1.3654326 103 1.3153005 104 1.3110788 105 1.2885991 106 1.3051655 107 1.3151547 108 1.3163824 109 1.3328680 110 1.3280408
In such a case how am I to decide which ones to take as a starting configurations ? Can you please give me an idea? On Sun, Jan 8, 2017 at 2:34 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/7/17 3:59 PM, abhisek Mondal wrote: > >> yes. 19 and 20. >> I have been able to modify distances.pl and it is running well I guess. >> It >> is taking a little time per configuration to process. >> >> Is there any way to know if distances.pl program terminates normally and >> calculations are successful ? >> >> > You won't get error messages and you will get a data file with distances > vs. configuration number. > > > -Justin > > On Sun, Jan 8, 2017 at 2:20 AM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 1/7/17 3:36 PM, abhisek Mondal wrote: >>> >>> Alright, I'm trying. >>>> Please tell me one thing, given the fact I want to analyse the >>>> protein-ligand pull scenario, what should be my choice during the >>>> prompt i >>>> get after executing "g_dist_mpi -s pull.tpr -f conf200.gro -n index.ndx >>>> -o >>>> all" >>>> >>>> Reading file pull.tpr, VERSION 4.6.2 (single precision) >>>> Group 0 ( System) has 2648311 elements >>>> Group 1 ( Protein) has 1693 elements >>>> Group 2 ( Protein-H) has 1301 elements >>>> Group 3 ( C-alpha) has 163 elements >>>> Group 4 ( Backbone) has 489 elements >>>> Group 5 ( MainChain) has 653 elements >>>> Group 6 ( MainChain+Cb) has 805 elements >>>> Group 7 ( MainChain+H) has 815 elements >>>> Group 8 ( SideChain) has 878 elements >>>> Group 9 ( SideChain-H) has 648 elements >>>> Group 10 ( Prot-Masses) has 1693 elements >>>> Group 11 ( non-Protein) has 2646618 elements >>>> Group 12 ( Other) has 15 elements >>>> Group 13 ( JZ4) has 15 elements >>>> Group 14 ( NA) has 1602 elements >>>> Group 15 ( CL) has 1608 elements >>>> Group 16 ( Water) has 2643393 elements >>>> Group 17 ( SOL) has 2643393 elements >>>> Group 18 ( non-Water) has 4918 elements >>>> Group 19 (Protein_chain_A) has 3210 elements >>>> Group 20 ( JZ4) has 15 elements >>>> Group 21 ( NA) has 1602 elements >>>> Group 22 ( CL) has 1608 elements >>>> Group 23 ( Water_and_ions) has 2646603 elements >>>> Group 24 ( r_1-163) has 5605 elements >>>> Group 25 ( r_164) has 39 elements >>>> >>>> Do I go with System ? I only need to see protein-ligand pull though. >>>> >>>> >>> What groups defined your reaction coordinate for the pulling? Those are >>> the groups you want. >>> >>> -Justin >>> >>> >>> Can you give me some suggestions ? >>> >>>> >>>> On Sun, Jan 8, 2017 at 1:58 AM, Justin Lemkul <jalem...@vt.edu> wrote: >>>> >>>> >>>> >>>>> On 1/7/17 3:24 PM, abhisek Mondal wrote: >>>>> >>>>> So I'm supposed to run "g_dist_mpi", right ? I'm on gromacs-4.6.2. >>>>> >>>>>> >>>>>> >>>>>> If you're using an old version, the syntax is totally different, so >>>>>> you >>>>>> >>>>> will have to make lots of changes to the script (or not use it at all). >>>>> >>>>> The catch here to analyze the COM distances between 2 pull groups. Am I >>>>> >>>>> getting that right ? >>>>>> >>>>>> >>>>>> Yes. >>>>>> >>>>> >>>>> -Justin >>>>> >>>>> >>>>> On Sun, Jan 8, 2017 at 1:46 AM, Justin Lemkul <jalem...@vt.edu> wrote: >>>>> >>>>> >>>>>> >>>>>> >>>>>> On 1/7/17 2:51 PM, abhisek Mondal wrote: >>>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> I'm pulling ligand out of protein using umbrella sampling method in >>>>>>>> gromacs-4.6.2. >>>>>>>> Using "trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep" command >>>>>>>> generated >>>>>>>> 500 different files (selected "SYSTEM" in interactive prompt, need >>>>>>>> to >>>>>>>> study >>>>>>>> protein and ligand simultaneously). But when I use "perl >>>>>>>> distances.pl >>>>>>>> " >>>>>>>> command I get none of the distances calculated. >>>>>>>> Following output was generated: >>>>>>>> >>>>>>>> ... >>>>>>>> Processing configuration 497... >>>>>>>> Processing configuration 498... >>>>>>>> Processing configuration 499... >>>>>>>> Processing configuration 500... >>>>>>>> readline() on closed filehandle IN at distances.pl line 16. >>>>>>>> Use of uninitialized value $distance in concatenation (.) or string >>>>>>>> at >>>>>>>> distances.pl line 30. >>>>>>>> readline() on closed filehandle IN at distances.pl line 16. >>>>>>>> Use of uninitialized value $distance in concatenation (.) or string >>>>>>>> at >>>>>>>> distances.pl line 30. >>>>>>>> readline() on closed filehandle IN at distances.pl line 16. >>>>>>>> Use of uninitialized value $distance in concatenation (.) or string >>>>>>>> at >>>>>>>> distances.pl line 30. >>>>>>>> readline() on closed filehandle IN at distances.pl line 16. >>>>>>>> Use of uninitialized value $distance in concatenation (.) or string >>>>>>>> at >>>>>>>> distances.pl line 30. >>>>>>>> readline() on closed filehandle IN at distances.pl line 16. >>>>>>>> ... >>>>>>>> >>>>>>>> >>>>>>>> Help me out here. What did go wrong ? >>>>>>>> >>>>>>>> >>>>>>>> gmx distance failed. Run gmx distance yourself and see what the >>>>>>>> error >>>>>>>> >>>>>>>> message is. The script just executes gmx distance and assumes >>>>>>> everything >>>>>>> works because it's designed for a tutorial. You may have to modify >>>>>>> it >>>>>>> to >>>>>>> get it to work in your system; you can't assume it is plug-and-play. >>>>>>> >>>>>>> -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? 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 *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.
