On 26/09/2011 9:04 PM, raj wrote:
Hello,
I have done simulations on cyclic peptide nanotubes and trying to
calculate the atomic concentration in the x and y axis, to measure the
diameter of the tube. I have tried using the g_rdf, but the results
are confusing to interpret. Here is the steps which I followed,
1. using trjconv, rotational and translational motions are removed
from the centered trajectory.
2. and then, g_rdf -f trj.xtc -s ref.gro -n index.ndx -o out.xvg (I
understood that the "-rdf atom" option is the default one and this
will calculate the atomic distribution in the x and y plane)
You need to indicate that you want the 2D analysis with a specific
option. Check out g_rdf -h
Mark
I am not sure whether the elimination of translational and rotational
motions is enough to calculate this property, should I have to align
the structure in the z axis using the PCA analysis?
Regards,
Raj.
--
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
