[gmx-users] Different results from gmx rms

Mark Abraham mark.j.abraham at gmail.com
Sat Mar 24 20:52:06 CET 2018


That depends on what you used to make minimize.tpr. If it's different from
the gro file then the rmsd will differ.


On Sat, Mar 24, 2018, 20:32 Dawid das <addiw7 at googlemail.com> wrote:

> Dear Gromacs Users,
> I get a bit different RMS when I use either minimize.tpr or
> start-crystal-structure.gro as a reference structure.
> This is definitely not because some atoms come across the
> boundary as simulation progresses (I checked that). What could be
> the reason? Does minimize.tpr use a different reference structure
> or has a different precision than start-crystal-structure.gro which
> was created starting from PDB crystal structure?
> Best wishes,
> Dawid Grabarek
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