Try this: trjconv -pbc mol -ur compact
And maybe you will find some useful answers here: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions I hope it helps -- Maurício Menegatti Rigo Núcleo de Bioinformática do Laboratório de Imunogenética Departamento de Genética Instituto de Biociências Universidade Federal do Rio Grande do Sul
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