@ Justin, Thanks. I fixed the index files like you suggested. I’m getting logical results now.
All the best, On Nov 2, 2013, at 7:11 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/2/13 7:01 PM, Xu Dong Huang wrote: >> Should I perhaps make an edit in the index file for group 1 to be particle 1 >> and 2, and group 2 = particle 2 and 3? >> > > No. If you want three different distances, you need three groups, as I said > in my previous message, and I even wrote the exact index file for you. > > -Justin > >> >> On Nov 2, 2013, at 6:50 PM, Xu Dong Huang <xudonghm...@gmail.com> wrote: >> >>> @ Gromacs users, >>> >>> so I did g_dist , and I’m confused by a couple of things. 1) why is it >>> asking me for 2 groups? I have my particles of interest under 1 type, >>> namely [ O1 ] 1 2 3, and nothing else. 2) I just picked the same >>> group twice, and the result is gives me in xvg is the following >>> There are no distances measured, that cannot be right. >>> >>> 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 >>> 20.0000000 0.0000000 0.0000000 0.0000000 0.0000000 >>> 40.0000000 0.0000000 0.0000000 0.0000000 0.0000000 >>> 60.0000000 0.0000000 0.0000000 0.0000000 0.0000000 >>> 80.0000000 0.0000000 0.0000000 0.0000000 0.0000000 >>> 100.0000000 0.0000000 0.0000000 0.0000000 0.0000000 >>> 120.0000000 0.0000000 0.0000000 0.0000000 0.0000000 >>> 140.0000000 0.0000000 0.0000000 0.0000000 0.0000000 >>> 160.0000000 0.0000000 0.0000000 0.0000000 0.0000000 >>> 180.0000000 0.0000000 0.0000000 0.0000000 0.0000000 >>> 200.0000000 0.0000000 0.0000000 0.0000000 0.0000000 >>> 220.0000000 0.0000000 0.0000000 0.0000000 0.0000000 >>> 240.0000000 0.0000000 0.0000000 0.0000000 0.0000000 >>> 260.0000000 0.0000000 0.0000000 0.0000000 0.0000000 >>> … >>> >>> Thanks in advance, >>> >>> Xu Huang >>> >>> >>> On Nov 2, 2013, at 6:35 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>>> >>>> >>>> On 11/2/13 6:29 PM, Xu Dong Huang wrote: >>>>> Dear All, >>>>> >>>>> My martini system has 3 particles in a chain, rest is martini water, and >>>>> I’m only interested in the bond length distribution of particle 1&2, 1&3 >>>>> and 2&3, and I execute the following: >>>>> g_bond -f npt.xtc -n index.ndx -o bonds.xvg >>>>> >>>>> I get the following error: >>>>> Total number of samples : 153 >>>>> Mean : 0.501255 >>>>> Standard deviation of the distribution: 0.152864 >>>>> Standard deviation of the mean : 0.0123583 >>>>> >>>>> Back Off! I just backed up bonds.xvg to ./#bonds.xvg.1# >>>>> >>>>> ------------------------------------------------------- >>>>> Program g_bond, VERSION 4.5.5 >>>>> Source code file: gmx_bond.c, line: 207 >>>>> >>>>> Fatal error: >>>>> No distribution... (i0 = 999, i1 = 1)? ? ! ! ? ! >>>>> For more information and tips for troubleshooting, please check the >>>>> GROMACS >>>>> website at http://www.gromacs.org/Documentation/Errors >>>>> >>>>> Upon inspecting my index files, I see that it defines my 3 particle group >>>>> as: >>>>> [ O1 ] >>>>> 1 2 3 >>>>> >>>>> Then I changed the particle group index file to >>>>> [ O1 ] >>>>> 1 2 >>>>> 2 3 >>>>> 1 3 >>>>> >>>>> And I’m still getting the same error. >>>>> >>>>> Any insights? >>>>> >>>> >>>> Use g_dist instead and measure the distances manually. g_analyze can then >>>> produce a distribution of those data. >>>> >>>> -Justin >>>> >>>> -- >>>> ================================================== >>>> >>>> Justin A. Lemkul, Ph.D. >>>> Postdoctoral Fellow >>>> >>>> Department of Pharmaceutical Sciences >>>> School of Pharmacy >>>> Health Sciences Facility II, Room 601 >>>> University of Maryland, Baltimore >>>> 20 Penn St. >>>> Baltimore, MD 21201 >>>> >>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>>> >>>> ================================================== >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>>> * Please don't post (un)subscribe requests to the list. Use the www >>>> interface or send it to gmx-users-requ...@gromacs.org. >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > ================================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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