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I have simulated a protein and ionized it with 0.15 NACL ( -neutral). keeping in mind the box dimensions and number of water molecules I have calculated the density of water which is combing around 0.9g/cm3. I have keep the parameters as defined in the lysozyme tutorial and RMSD graph was stable. Shouldn’t the water density must be 1?
i am confused does this mean my system wasn’t solvated properly ?
what was the duration of the simulation? this is ‘ok’.
Your system is not homogeneous so a difference with the density of pure water is expected. More importantly, water density in simulations depend on the water model. Some are known to under/overestimate it, and the magnitude of the error depends on the temperature as well.
Check the average density and the simulation box side lengths over time to see whether they are converging or not (are they reaching a plateau?). This gives you a good insight on the status of the box. And check the density of the water against the expected computational density, either from reading the original paper where they developed the water model or from one (of the many) reviews about differences between water models.