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
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
