Hi, I'm facing a problem with GROMACS that appears pretty simple, actually. I'm trying to set a dodecahedron box but all I can get is a triclinic box. For that, I'm using the following line: * editconf -f pMHC -bt dodecahedron -o -d 1 *
Am I doing something wrong?? Another problem, different from this one, is that my protein, during the simulation, is escaping/comming off/"running away" (sorry I'm butchering the english) from the water box. I tried to use periodic boundaries conditions, but didn't work (I added a line in my .mdp file - pbc = xyz). Someone could help me with that, please? I really appreciate ! -- Maurício Menegatti Rigo Núcleo de Bioinformática do Laboratório de Imunogenética Departamento de Genética Instituto de Biociências Universidade Federal do Rio Grande do Sul - Brazil
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