def stage_2(self, instance): k2 = Kernel(name="md.gromacs") k2.link_input_data = ['$STAGE_1/in.tpr > in.tpr'] k2.executable = ['path/to/gromacs/gmx'] k2.arguments = ['mdrun', '-s', 'in.tpr', '-deffnm', 'out'] k2.cores = 1 return k2
def stage_1(self, instance): k1 = Kernel(name="md.gromacs") k1.upload_input_data = ['in.gro', 'in.top', '*.itp', 'in.mdp'] k1.executable = ['path/to/gromacs/gmx'] k1.arguments = ['grompp', '-f', 'in.mdp', '-c', 'in.gro', '-o', 'in.tpr', '-p', 'in.top'] k1.cores = 1 return k1
def stage_1(self, instance): k1 = Kernel(name="md.gromacs") k1.upload_input_data = ['in.gro', 'in.top', '*.itp', 'in.mdp'] k1.executable = ['path/to/gromacs/gmx'] k1.arguments = [ 'grompp', '-f', 'in.mdp', '-c', 'in.gro', '-o', 'in.tpr', '-p', 'in.top' ] k1.cores = 1 return k1