[gmx-users] molecule broken

Justin A. Lemkul jalemkul at vt.edu
Thu Jun 19 12:38:06 CEST 2008

This is probably a visualization artifact, since mdrun does not make a 
break bonds to generate fragmented molecules.


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


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