[gmx-users] Regarding RMSD analysis result

[Felipe Pineda, PhD]

It looks for me like the known pbc effect others already pointed to. If 
you have just a protein-ligand complex (+ water and counterions of 
course) it's relatively easy to manually (a piece of code would do it) 
bring the ligand to the correct position in the frames showing an 
abnormally high value by subtracting half the x/y dimension of the box 
from its coordinates and re-calculate the rmsd , but I think trjconv 
would do it as well.

Felipe

On 09/25/2012 09:22 AM, naga sundar wrote:
> Dear justin
>
>                  http://rmsdnagasundaram.blogspot.in/. This is the link to
> my rmsd graph. Plz check it once and suggest me.
>
>
> Thanks
>