Sincere apologies... I have uploaded the files here... https://drive.google.com/drive/folders/0B6O-L5Y7BiGJT29hSGlEWTM3Zk0?usp=sharing
I'm running another pull experiment with "pull_rate1 =0.01". On Sun, Jan 8, 2017 at 10:23 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/8/17 1:52 AM, abhisek Mondal wrote: > >> Alright. I'm attaching md_pull.mdp and sumary_distances.dat file. >> >> May be I have set pulling rate very low. Anyway have a look. >> >> > The list does not accept attachments (if I had a nickel for every time I > said this...) so upload the files somewhere and provide a link. > > > -Justin > > >> On Sun, Jan 8, 2017 at 6:03 AM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 1/7/17 5:20 PM, abhisek Mondal wrote: >>> >>> 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? >>>> >>>> >>>> It would help to have a full explanation of what you're doing, including >>> .mdp files. Getting partial details along the way makes it hard to give >>> any useful advice. >>> >>> It looks like your species just oscillated over a range of 0.1 nm, which >>> achieves very little, if anything, and certainly nothing resembling >>> dissociation between the two. >>> >>> >>> -Justin >>> >>> 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. >>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>> ================================================== >>> >>> 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.