HI All, I ran some membrane protein simulations and got some strange results. The RMSD (~.18 nm) of the protein equilibrated quite nicely but when I look at the trajectory the protein seems to be diffusing way to much over 20ns. The protein has about 1000 AA. I calculated the KE of the protein, lipid, and water and got a KE that was 1.5RT, 1.2RT, and .8RT respectively. My T is 298K. My COM removal and T-coupling is for the whole system. I am running 3.3.1. Is there a problem with T-coupling and COM removal on the whole system?
Thanks, Ilya -- Ilya Chorny Ph.D.
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