[gmx-users] Different results from gmx rms

[Dawid das]

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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