This is probably a visualization artifact, since mdrun does not make a
break bonds to generate fragmented molecules.
-Justin
Nguyen Hoang Phuong wrote:
Dear All,
I am running a simulation for a RNA system using 50 cpus with gromacs
3.3.1. At some frames, my molecule is broken, that is parts of the
molecule are on opposite sides of the periodic box. This problem was
reported sometime ago (Nov. 2006) and David suggested to submit the
bugzilla. Is this problem caused by parallel job? If that is the case,
was the problem fixed? The molecule is whole initially. Thanks.
Phuong
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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