[gmx-users] RMSD plot

[Mark Abraham]

minnale wrote:
> 
> If I use the command in this way with option -mir insted of -o
> 
> g_rms -f 9ns.xtc -n r20-50.ndx -mir mirror.xvg -pbc -s min.gro
>       selected r_20-50 for least square fit group
>       selected c-alpha for RMSD calculation
> 
> if I plot a graph by using mirror.xvg file there is no fluctuations 
> after 4ns to 9ns I can say system is almost stabilised, but if i use -o 
> option RMSD values are quite vary and system not yet stable even at 9ns
> so shall i stop the simulation or continue the simulation some more time 
> as Justin said.
> sorry for the asking trivial questions.
> Thanks for your appreciation 

>  >have you mirrored your trajectory  back to a normal box?
>  >Have you inspected it visually, does it always stay inside the box?
> 
>  >If not use trjconv -pbc nojump -fit rot+trans

Florian wasn't suggesting using the "-mir" flag to g_rms, but rather to 
use trjconv.

Your results suggest that you haven't merely added the use of the "-mir" 
option, for it's not possible for a trajectory to fluctuate with respect 
to a single structure, and to be stable with respect to that structure's 
mirror image.

Mark