DNA methyl transferase1 (Dnmt1) preferentially methylates hemi-methylated DNA. Upon the methylation of DNA, a methyl group is provided by S-adenosyl-L-methionine (SAM), which becomes the product S-adenosyl-L-homocysteine (SAH). We performed molecular dynamics (MD) simulations to trace the dynamics of SAM and address SAH in inactivated Dnmt1 in mice. Our MD simulations found that SAM was more stable than SAH under the inactivated Dnmtl environment, indicating that an exchange of cofactors might occur in the inactivation state before the next methylation process.