[gmx-users] Different results from gmx rms

[Justin Lemkul]

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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