[gmx-users] RMSF error when fitting to average structure
Dear all, I have a 70 ns trajectory for which the last 60 ns appears to be equilibrated. I'm attempting to create a plot of RMSF but I want to align it to the equilibrated structure, not the starting structure. I first ran g_rmsf using the starting structure as the reference structure over only the last 60 ns and output the average structure (with B-factor column) using the -ox flag. I would now like to use this average, equilibrium structure as the reference structure for fitting the entire trajectory. When I try and use this average structure as a reference structure with the -s flag, I get the following error: WARNING: if there are broken molecules in the trajectory file, they can not be made whole without a run input file I'm not sure if the broken molecule it's referring to is the average structure, which I presume could be broken due to the unnatural bond lengths and angles resulting from averaging or if there's a problem trying to use a pdb file (which is the only -ox output file option) instead of a .tpr file, which is the format of the original starting structure, which worked. Does anyone have a suggestion as to how to obtain this rmsf plot? Thank you, Tom -- View this message in context: http://gromacs.5086.n6.nabble.com/RMSF-error-when-fitting-to-average-structure-tp5000251.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
[gmx-users] Re: RMSF error when fitting to average structure
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. 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? Thanks, Tom -- View this message in context: http://gromacs.5086.n6.nabble.com/RMSF-error-when-fitting-to-average-structure-tp5000251p5000258.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
[gmx-users] Re: RMSF error when fitting to average structure
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? Thanks, Tom -- View this message in context: http://gromacs.5086.n6.nabble.com/RMSF-error-when-fitting-to-average-structure-tp5000251p5000260.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
[gmx-users] Re: RMSF error when fitting to average structure
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. -- View this message in context: http://gromacs.5086.n6.nabble.com/RMSF-error-when-fitting-to-average-structure-tp5000251p5000262.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
[gmx-users] Re: RMSF error when fitting to average structure
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? -- View this message in context: http://gromacs.5086.n6.nabble.com/RMSF-error-when-fitting-to-average-structure-tp5000251p5000264.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
[gmx-users] Re: Distance restraints not working
There are a few possibilities. 1. Numbering in [distance_restraints] is not based on .gro numbering. The atom numbers supplied are only relevant within the [moleculetype] to which they belong, much like [position_restraints]. Also make sure that the [distance_restraints] block is in the correct location in the topology. 2. You've omitted the dihre_fc keyword, though it is set to 1000 by default. Check the mdout.mdp file or your .tpr file to ensure that you have a sensible value here. Setting values of fac that high are unnecessary. Thanks for your help. I have it working now. It actually turned out to be a typo. I have an unrelated question though. After running the temperature and pressure equilibration, grompp tells me my md run will produce ~150 GB of data. I'd really like to avoid such an enormous amount of data. The system is ~300,000 atoms and I will be running 20 ns of simulation (~3 days on our cluster according to the equilibration output). Can I simply change the output control from saving the various files at every 2 ps to every, say, 20 ps? I realize it's a large jump compared to 2 ps, but 150 GB is a lot of data. Will changing the output control so drastically adversely affect the simulation in any way? -Tom -- View this message in context: http://gromacs.5086.n6.nabble.com/Distance-restraints-not-working-tp4997654p4997692.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-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
