No, using a trajectory file with g_hydorder hasn't made any difference. The error is still the same.
When I use g_polystat, I use the following command: g_polystat_d -f file.xtc -s file.tpr -n polymer_backbone.ndx -p persist.xvg -o polystat.xvg Note: Using "polymer_backbone.ndx" yields fewer polymers with nan issues, than using the whole polymer structure in an index file. Kind Regards, Alaina ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 01 May 2013 10:58 To: Discussion list for GROMACS users Subject: Re: [gmx-users] help with g_hydorder and g_polystat On 4/30/13 9:00 PM, Emmanuel, Alaina wrote: > Hello Justin, > > My mdp file shows that the pbc was set to xyz. > Instead of analyzing a coordinate file, does it work with a trajectory? Regarding g_polystat and the nan's, what command are you issuing? -Justin > > Kind Regards, > > Alaina > > ________________________________________ > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf > of Justin Lemkul [jalem...@vt.edu] > Sent: 30 April 2013 16:10 > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] help with g_hydorder and g_polystat > > On 4/30/13 6:24 AM, Emmanuel, Alaina wrote: >> Dear All, >> >> I'm fairly new to gromacs and having a bit of problem with the g_hydorder >> and g_polystat. Thanks in advanced for your time. >> >> For g_hydorder, >> I get a fatal error when I type the following command: >> g_hydorder_d -f file.gro -s file.tpr -n waters.ndx -o file1.xpm file2.xpm >> Error: >> Internal error in pbc_dx, set pbc has nor been called >> For more information.. >> ---------------------------------------- >> >> I'm not sure what this means. It seems to be implying that I don't have a >> box around my polymer, but the gro file clearly shows that my box is 4.94 x >> 4.94 x 4.94. Any ideas? >> > > What is your setting for the pbc keyword in the .mdp file? > >> >> For g_polystat, I'm a bit worried about the persistence lengths that I get >> for short polymers. With repeat units smaller than 50 these usually show >> "nan" values, that cannot be plotted. From reading the gmx threads I've >> found that Nan stands for "Not a Number", but why do these "nan" values >> appear and how can I prevent it so that I can read in my results? >> > > This could be an underlying problem related to the above interpretation of > periodicity. We don't have enough information to say for sure yet. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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
