[gmx-users] RMSF error when fitting to average structure

Justin Lemkul jalemkul at vt.edu
Thu Aug 16 19:02:14 CEST 2012

On 8/16/12 10:13 AM, tdgrant1 wrote:
> 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?

The warning about broken molecules relates to the trajectory (as stated in the 
message), so periodicity effects are not accounted for if you are not using a 
.tpr file.  Thus you could get erroneous results unless you have already 
corrected for PBC effects using trjconv before running g_rmsf.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list