shahid nayeem wrote:
Dear All
I want to calculate RMSD of one side chain residue from simulation
trajectory after full backbone alignment as well as translating to
coincide CA of the residue of interest. Is it possible to do with
g_rms both backbone alignment as well as translating to coincide CA.
Least-squares fitting is performed on whatever group you choose (i.e. backbone),
and the calculation group can then be whatever you want. You can use trjconv to
do translational fitting, but I don't know that you can force g_rms to always
align this certain atom and still perform a backbone fit; these two may work
against one another, even if the difference is small.
Another clarification is that in gromacs g_cluster how can I use
greedy algorithm for clustering.
What is a "greedy" algorithm? The available methods are described in the manual
and/or g_cluster -h.
-Justin
Shahid Nayeem
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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
