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

Peter C. Lai pcl at uab.edu
Fri Apr 6 09:02:23 CEST 2012

Because if all you did to generate the 2nd tpr file was tpbconv -extend, then
both tpr files are same *except* for the simulation time.
(gmxdump should prove it)

On 2012-04-05 11:57:41PM -0700, 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?
> Cheers,
> Acoot   

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