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
in
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.
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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
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?
T
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
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 i
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