thanks again. I did the recommended option in the grompp command , but there a problem with minimization step. the error is "Water molecule starting at atom x can not be settled". I checked the previous emails and I did a few things but I can't solve it. In the previous emails, it was recommended to reduce the timestep and I used (0.1, 0.01, 0.001, 0.0001) steps. Also I checked the produced pdb files after that the programs stopped and I see that some of the water molecules stretch out along the box. I don't know how to fix this problem? -- Gromacs Users mailing list
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