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?
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 > -- 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
