[gmx-users] Different results from gmx rms

Mark Abraham mark.j.abraham at gmail.com
Sat Mar 24 21:59:04 CET 2018


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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