GROMACS modification: Yes/No
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I am simulation water tip4p diffusion in polymer. I want to be sure that my system has reached equilibrium state. Actually, I want to know after what time the analysis is reliable to get a suitable time for simulation? What kind of analysis can be used for this purpose?
Thank you very much
First you need to make sure system’s temperature, pressure and energies are equilibrated, which can be checked using gmx energy. Plot these properties, see if you reached equilibrium. In addition to these, you might want to check radius of gyration vs. time convergence for polymeric system.
Thank you very much for your response. I have another question.Does Velocity Autocorrelation Function provide good results for prediction of equilibrium? I heard when it converges to zero we can grantee
Thank you again for your reply
I never used velocity autocorrelation to determine equilibrium state, I can’t comment. Velocity autocorrelation can be used to calculate dynamic properties such as, diffusion coefficient, viscosity.
Hello dear Masrul
Thank you very much for your reply.