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 list gmx-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