[gmx-users] How to avoid the infinite potential energy in simulations of dimers?

[Qing Liu]

Dear Gromacs users,
      I run some simulations of dimers, a protein binding another protein. When these simulations step into equilibriumstages,  they will crash with the following:





                  Step 2029: The total potential energy is nan, which is not finite. The LJ and
                  electrostatic contributions to the energy are 746119 and -5.71229e+06,
                  respectively. A non-finite potential energy can be caused by overlapping
                 interactions in bonded interactions or very large or Nan coordinate values.
                Usually this is caused by a badly- or non-equilibrated initial configuration,
                 incorrect interactions or parameters in the topology.
       

      I try to turn on soft-core potential but it's not working. However, the simulations of monomers with same mdp files are normal.  How should I do to solve the problem?






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Best wishes, 

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Qing Liu

Fudan Univ.

Mobile: +86—13358129621

E-mail: 15110700076 at fudan.edu.cn