[gmx-users] (无主题)

吴修聪 wuxc1230 at 126.com
Fri Mar 8 15:21:13 CET 2019

Dear gmx-users, i am trying to use GROMACS to simulate an infinite system, a triple helix polymer(three chains), but a tricky problem challenged me that different chains jump between the box in the trajectory. I tried to use different options for pbc,  like whole/mol/nojump/atom/res. It still can't be solved. Since the polymer is bonded by command to become an infinite system, the box is a little smaller than the monomer. With pbc - atom or res or nojump, the atoms are wrongly bonded in the trj, with pbc -mol, the chain jump between the box. I guess it's because the inconsistent shifts. Can anyone help me solve this problem? Best regards Xiucong

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