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

[tdgrant1]

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?



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