[gmx-users] the g_rms function after we trjcat the trajectory files before and after extension

[Mark Abraham]

On 6/04/2012 4:57 PM, Acoot Brett wrote:
> Dear All,
> Before and after extention we have 2 trajectorty files, and by trjcat 
> we got we, then we can do the g_rms
> g_rms -s *.tpr -f *_noPBC.xtc -o rmsd.xvg -tu ns
> But here for the g_rms command I find no matter whether we use the  
> *.tpr of the initiation of the production MD, or the *.tpr for the 
> initiation of the extension part, the rmsd.xvg curves seems same.
> Will you please give some comment on it?

If you used tpbconv -extend, or similar, then the two .tpr files contain 
the same structure, and so the reference structure for g_rms is the 
same. The starting configuration for MD is determined by the contents of 
the -cpi file, if given, and the .tpr file only as a fallback.

Mark
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