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.
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. > -- Abhisek Mondal *Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA*
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