bhargavi ch wrote:
hi..
the sudden shoot up was observed in the RMS because of molecule breakage
into monomer and dimer.we have also mutated some surface hydrophobic
aminoacid and dint observe shoot up in any of the mutation. We have
also observed the same shoot in the case of X ray crystallographic
structure of template protein, when we did 10 ps simulation. what are
the parameters which we need to take to avoid such shoot up??
As Mark pointed out, based on your original description, you are probably seeing
PBC effects. Use trjconv to remove periodicity, and analyze the RMSD again.
-Justin
thanx
Bhargavi
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
