kecy...@sina.com wrote:
Hello, I use the 2D periodic boundary along the x and y axises, it has a
strange thing. my solvent is dodecane, I view the output trajectory in
the VMD, for one molecule, it has some part in
the left(top), and some in the right(bottom), it still connections to
each other, how to solve this problem?
Sounds to me like the normal outcome of PBC:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
-Justin
Thank you !
--
========================================
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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