Frequently Asked Questions (FAQ)

For now, there are no questions.

How to Get Help

MiMiC is distributed for free and without any guarantee of reliability, accuracy, or suitability for any particular purpose. No obligation to provide technical support is expressed or implied.

We have a discussion group for our user community. We encourage you to be comprehensive in providing explanations and to share all relevant background information that could facilitate better assistance. Please be aware that although we strive to assist you to the best of our ability, we are not equipped to offer support for external programs, such as CPMD and GROMACS. For bug reports, please visit our GitLab page.

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Before you decide to seek help, please make sure that your issue is not a common one by consulting the FAQ.

Known Issues

In this section, a list of known issues in the latest version of MiMiC is reported, together with suggestions for workarounds. Each issue is reported using the following structure when applicable:

  • Description: Brief description of the problem.

  • Identification: Explanation of the “symptoms” or scenarios in which users might encounter the issue.

  • Workaround: Suggestions on how to address the issue until it is fixed in MiMiC.

Constraints in GROMACS

  • Description: GROMACS allows the user to specify a variety of constraints in a .mdp file. In particular, constraining bond with hydrogens is common using the keyword constraints = h-bonds. However, this functionality is not currently supported in MiMiC.

  • Identification: Using constraints = h-bonds will cause problems in the constraints solver, resulting in an unphysical elongation of bonds that include hydrogens.

  • Workaround: Use constraints = none in the .mdp file. If needed, specify all constraints for your system in the CPMD input (CONSTRAINT keyword in the &ATOM section; check the CPMD manual for more details). Note that the atom indices need to be the ones in CPMD. For this purpose, MiMiCPy CPMDid can be helpful.

Discontinuities in energy and temperature

  • Description: Energy and temperature may present discontinuities when the dynamic load balancing is turned off in GROMACS.

  • Identification: From visual inspection of the energy or temperature, it is possible to observe “jumps”, after which those quantities keep evolving “unperturbed”. To confirm that those discontinuities are related to this issue (and not, for example, to a badly equilibrated system), it is possible to check the GROMACS .log file: a message like step N Turning off dynamic load balancing, because it is degrading performance will be printed, and the step number N will correspond to the step where the discontinuity point can be observed in the energy during the trajectory.

  • Workaround: Dynamic load balancing can be turned off in GROMACS mdrun with the option -dlb no. Turning off dynamic load balancing in GROMACS is not expected to have a significant impact on the performance in a MiMiC-based QM/MM MD simulation.

Available water models

Currently, MiMiC only supports three-site water models (e.g., TIP3P, SPC), both rigid and flexible. Water models with more than three sites (e.g. TIP4P, TIP5P) are currently not supported.