[gmx-users] Regarding RMSD analysis result
Felipe Pineda, PhD
luis.pinedadecastro at lnu.se
Tue Sep 25 09:45:55 CEST 2012
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.
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.
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