Re: [gmx-users] Re: RMSF error when fitting to average structure
On 8/16/12 3:19 PM, tdgrant1 wrote: Hi Justin, I did indeed correct for periodic boundary conditions prior to running rmsf, so I'm not sure what the problem would be there. The message you got was a warning, not an error. The warning is generic and is printed by any Gromacs program that does not receive a .tpr file passed to the -s flag. It is not necessarily indicative of any problem but is written to be helpful to the user. Is there any way of producing an average structure from rmsf (or any other program for that matter) that is not output as a .pdb file but as a .tpr file? You can easily produce a .tpr file from any coordinate file using an existing topology and .mdp file. Coordinate files are not generally written in .tpr format. -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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
Re: [gmx-users] Re: RMSF error when fitting to average structure
On 8/16/12 3:54 PM, tdgrant1 wrote: Oh okay, thanks. I didn't realize warnings were just that, only warnings and didn't stop the program. The program did not finish however, and the problem was a Segmentation Fault. The output literally was: Select a group: 0 Selected 0: 'System' Reading frame 0 time0.000 WARNING: if there are broken molecules in the trajectory file, they can not be made whole without a run input file Segmentation fault Could this be related to the input file, or do you think this is something else entirely? Depending on how many atoms are in the entire system (is it a fully solvated protein, anything else?) then you probably ran out of memory. These analyses are normally performed only on the solute of interest or a subset of those atoms (like a protein backbone). -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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
Re: [gmx-users] Re: RMSF error when fitting to average structure
On 8/16/12 4:11 PM, tdgrant1 wrote: This System as described by group 0 in the previous message is actually only the solute, a protein-tRNA complex of ~15000 atoms. I tried running only the backbone and even only c-alphas (808 atoms total) and I still received a segmentation fault. Do the number of atoms in the structure file passed to -s and the number of atoms in the trajectory passed to -f match? -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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
Re: [gmx-users] Re: RMSF error when fitting to average structure
On 8/16/12 4:19 PM, tdgrant1 wrote: No they do not. The trajectory contains all the atoms, including the solvent (~300,000 atoms), whereas the structure passed to -s is the averaged structure from the last 60ns of simulation and only includes the non-solvent atoms (~15,000). Should I rerun rmsf on the last 60ns but select System instead of non-solvent, and then use that averaged structure to pass to the -s flag? I don't see how getting the average structure of a 300k atom system is meaningful - that will certainly chew up lots of memory ;) What I would suggest is one of the following: 1. Create a .tpr file with your averaged structure from an existing topology and run g_rmsf. 2. Use trjconv to create a subset trajectory (.xtc) that matches the number of atoms in the reference structure. 3. Avoid ever choosing System for analysis - choose the backbone or whatever custom index group you wish to use. I don't see an inherent problem with using the System in the reference structure (your RNA) but you never know when there's some curious mismatch in the interpretation down the line. Could be a bug, but I'm not prepared to believe that yet from the evidence at hand. -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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
