Chih-Ying Lin wrote:
Hi With the periodic boundary condition, all the recorded coordinates of
the atom are within the simulation box. To calculate the MSD, the
movement of the center mass of the molecules between this time step with
the next time step is calculated without considering the periodic
boundary condition. But all the recorded coordinates of the atom are
within the simulation box after considering the periodic boundary condition.
Does g_msd remove the effect of the periodic boundary condition ?
Yes.
So, how can I remove the periodic boundary condition to get the truly
movement of the atoms between the two time steps ? Thank you Lin
No need. See above.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
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
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