On 4/24/13 3:26 AM, James Starlight wrote:
The only possible way to view representation of the configuration volume
of the ligand was the representation of all frames of the ligand along the
trajectory. By the way its not quite understand for me in one case the
measurement of the diffusion coefficient could be better than MSD which is
the measure of the random displacement of the particle itself. ( my current
taks is the examination of the ligand mobility as the rigid-body within
ligand-binding-cavity).
Also I wounder to know about some possible way to measure dynamics of the
non-covalent bonding along the trajectories.
E.g I've defined in index file all polar and aromatic residues of the
ligand-binding pocket. IS there any way to calculate all possible bonds (I
want to measure the lifetime of that bonds as well as its occurrence in
case of different ligands) between ligand and that side-chains along the
trajectory ?
What you're describing are nonbonded interactions, not bonds. There are a
variety of quantities you can measure, like hydrogen bonds, contacts, etc. You
can post-process to get various autocorrelations and lifetimes. Again, Chapter
8 is your friend here.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
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
