[gmx-users] molecule broken

Nguyen Hoang Phuong phuong at theochem.uni-frankfurt.de
Thu Jun 19 11:56:37 CEST 2008

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.


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