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

[Justin Lemkul]

On 2/21/20 5:11 AM, Qing Liu wrote:
> 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:
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>                    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?
>

Your initial configuration is unreasonable as you have a massive LJ 
repulsion. How did you construct the coordinates of the system? Likely 
energy minimization will have reported unreasonable forces, as well.

-Justin

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Justin A. Lemkul, Ph.D.
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