I am currently simulating some protein-protein complexes. I am getting a positive potential for a few complexes. Please let me know how to make it negative or if I can proceed with equilibration. I am simulating in water with 0.15M NaCl at 310K. I have the number of steps as 6000 instead of 50000 as the 50000 is giving other errors.
The minimimsation anyways stops as soon as F<1000. How to extent minimisation even after F<1000?
For other complexes, I am getting the following error after npt:
Pressure scaling more than 1%. This may mean your system is not yet equilibrated. Use of Parrinello-Rahman pressure coupling during equilibration can lead to simulation instability, and is discouraged.
I saw this post (Pressure scaling more than 1%) about using Berendsen. So how is this carried out. First change to berendsen then what output file to use as the input for Parrinello-Rahman?
Do you have the force tolerance set to 1000? If so, lower it.
Force pressure coupling we always advise to use the c-rescale barostat. That message about using Berendsen is outdated and we have recently changed it to suggeset c-rescale.
Last time you mentioned about lowering the force tolerance. I did it and I am successfully getting a potential negative for some structure. However, there are some with potential still showing positive even after I decreased emtol to 10 kJ/mol/nm. Could you please let me know if I can decrease emtol to a negative value? Thank you.
