RyR1 is a calcium release channel in the sarcoplasmic reticulum which is involved in excitation-contraction coupling of skeletal muscle. Mutations in RyR1 are known to cause malignant hyperthermia. We have recently developed a RyR1 inhibitor, Cpd1, for the treatment of malignant hyperthermia. Although Cpd1 is predicted to bind to the P1 domain of RyR1, the cryo-EM structure of RyR1 complexed with Cpd1 has not been obtained yet, due to low resolution of the P1 domain. Here, we performed molecular dynamics simulations to predict the Cpd1-bound structure of the P1 domain. The simulations were performed using the molecular dynamics program myPresto with different initial coordinates and simulation time. The stability of the output structures was evaluated by the amino acid interactions, and the convergence of the conformational change was evaluated by the RMSD plot. We obtained a stable complex structure of P1 with Cpd1from several initial coordinates with longer simulation time. Interestingly, the structure of P1 complexed with Cpd1 was significantly different from the initial conformation without Cpd1, suggesting that Cpd1 may induce a significant conformational change of the P1 domain.