[gmx-users] a question about gromacs

里梦 limeng9505 at tom.com
Wed Jul 4 03:42:57 CEST 2007

  I have an urgent question to ask for help.  I have created a new molecule by gromacs and one dihedral of this molecule is designed as 120 degrees. During the simulation, the dihedral varied from 118 to 122 degrees, and the average is about 120 degrees. I know this is because that the dihedral is defined by harmonic potential, but I want to know is this precision enough for the simulation. I mean that is the dihedral varying from 118 to 122 proper, or should I constrain this dihedral changing from 119 to 121?
  I am looking forward to your reply! Thanks!
                                                          Meng Li

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