[gmx-users] Re: Re: RMSD VS. parallel simulation (Mark Abraham)
Mark.Abraham at anu.edu.au
Mon Apr 7 08:30:40 CEST 2008
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.
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