Hello Justin, My mdp file shows that the pbc was set to xyz.
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 -- 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
