[gmx-users] Different results from gmx rms

[Dawid das]

I checked again and it didn't.

2018-03-24 21:58 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:

> Hi,
>
> Did gmx rms warn you suitably that it was making guesses about masses?
>
> Mark
>
> On Sat, Mar 24, 2018, 21:07 Dawid das <addiw7 at googlemail.com> wrote:
>
> > Thank you Justin. In fact, editconf gave me .gro file with the same
> > coordinates as starting ones, so it must be due to masses.
> >
> > I checked again with -nowm and now both start-cryst-structure.gro and
> > minimize.tpr give me the same RMS, so these must be
> > the masses. I added my own amino acid residue definition and plausibly
> for
> > my new non-hydrogen atoms, the guessed mass
> > is that of carbon, while there are carbon, nitrogen, oxygen atoms.
> >
> > Best regards,
> > Dawid
> >
> > 2018-03-24 20:56 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
> >
> > >
> > >
> > > On 3/24/18 3:55 PM, Dawid das wrote:
> > >
> > >> Hi,
> > >> well actually I used the same file to make minimize.tpr
> > >>
> > >
> > > Verify that the coordinates are the same by using editconf to extract
> > > coordinates from the .tpr file in .gro format, and then if they are the
> > > same, the difference likely comes from the fact that masses are guessed
> > > when providing a .gro file as a reference, whereas the precise values
> are
> > > used when providing a .tpr file. There may be small differences there
> > with
> > > respect to precision, which therefore influences the least-squares
> > fitting.
> > >
> > > -Justin
> > >
> > >
> > > Dawid
> > >>
> > >> 2018-03-24 20:51 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:
> > >>
> > >> Hi,
> > >>>
> > >>> That depends on what you used to make minimize.tpr. If it's different
> > >>> from
> > >>> the gro file then the rmsd will differ.
> > >>>
> > >>> Mark
> > >>>
> > >>> 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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> > > --
> > > ==================================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Assistant Professor
> > > Virginia Tech Department of Biochemistry
> > >
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