[gmx-users] Re: Re: RMSD VS. parallel simulation (Mark Abraham)

[Mark Abraham]

Dechang Li wrote:

>>>>>   In the 16 CPUs simulation, the RMSD of protein at t=0 was about
>>>>> 0.1 nm, why not equal to zero? I used the initial structure for the
>>>>> least squares fit.
>>>> If you've done an equilibration or EM, the structure can have changed 
>>>> during that.
>>>    I mean the initial structure is the structure I used to generate the 
>>> .tpr file for mdrun_mpi. 
>> What were your command lines, choices for groups and outputs? The most
>> likely simple explanation is that you haven't done what you think you've
>> done :-)
> 
>    My command lines:
>   
>    g_rms -s md.tpr -f md.trr -o rms_protein.xvg -n index.ndx
> 
>    choices for groups:
>    
>     Select group for least squares fit: Protein
>     Select group for RMSD calculation:  Protein

Have you used gmxcheck to see if the coordinates in md.tpr match the
first frame of md.trr?

If you're using constraints then these are probably applied before
writing the t=0 md.trr frame, check that.

You have managed to avoid one common mistake, which would be to use a
.gro or .pdb file as input to -s, and not to realise that these are
reduced-precision file formats and thus differences from rounding errors
are to be expected.

Mark