I’m dealing with a homodimer and I’m trying to calculate the entropy of association of the two monomers. Each monomer has 125 residues. I’ve conducted 3 calculations for the last 40 ns of a 100 ns trajectory, using the same traj.nc, topologies and input file. The number of frames in each calculation was 10, 20 and 40 frames respectively.
The results are summarised below:
1st calculation - 10 frames
DELTA S: -62.8801 Total time taken: 29.583 min.
2nd calculation - 20 frames
DELTA S: -89.2849 Total time taken: 30.667 min.
3rd calculation - 40 frames
DELTA S: -136.5619 Total time taken: 30.714 min.
The differences observed are due to the vibrational component of the entropy (in all 3 calculations, the translational and rotational components are almost identical).
I’m aware of the shortcoming of such calculations but I have problems in understanding the very large variation in the vibrational component of entropy. Could it be that the time interval between consecutive frames is too short? If this is the case, how does one determine an “optimum” interval?
Any explanation/suggestions, etc would be much appreciated
Regards
George
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Received on Tue Apr 18 2017 - 05:00:03 PDT
