ahmet yıldırım wrote:
Dear Justin,
You said "You didn't properly account for PBC. Watch the trajectory -
you should see distinct jumps across the box." for attached figure.
What should I do?
Exactly as I said. Watch the trajectory to see if my guess is right. If the
molecule is dancing back and forth across PBC, it explains what you're seeing
with the RMSD.
Fix the PBC issues with trjconv, if that is indeed the case.
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
-Justin
--
Ahmet YILDIRIM
------------------------------------------------------------------------
--
========================================
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
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