Required for NPT Step Issue with Protein 1QS4 (4 Waters and Mg²⁺ in Active Site)

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1

am currently working on a MD simulation involving the protein 1QS4 with GROMACS, which contains four crystallographic water molecules and a Mg²⁺ ion in its active site. I have performed QM/MM calculations using Gaussian to generate the topology and GRO file for my system.

To stabilize the active site, I defined a position restraint file (posre.itp) for the protein, the four waters, and the Mg²⁺ ion, excluding hydrogen atoms. Using this setup, I could completed the energy minimization (EM) and NVT equilibration steps.

However, during the NPT equilibration step, I encountered LINC warnings, and the simulation stops. I have taken the following steps to resolve the issue, but without success:

  1. Changed the barostat to Berendsen.
  2. Increased the pressure coupling time constant (tau_p) to 5 ps.

Despite these changes, the issue persists. I am using GROMACS version 2018 for my simulations.

I suspect the issue might be related to the restrained water molecules or Mg²⁺ ion in the active site during NPT equilibration, but I am uncertain how to proceed.
I will be grateful someone can guide me how to fix my problem

2

This seems to be a duplicate of NPT Step Issue with Protein 1QS4 (4 Waters and Mg²⁺ in Active Site). Please, don’t make multiple posts with the same topic. Be patient, it can take a long time before anyone has time to help you. If it has taken multiple weeks without a reply, you might make another post in the same thread to bring more attention to it, perhaps your post has not been seen. Another explanation might be that no-one knows.

3

Thanks alot!
Yes, sure, it was a first time I posted a question, I didn’t know how it works
Best regards
Shayesteh