Dear All
I have computed atomic fluctuation correlation function for a particular atom of a protein system based on the trajectory file generated using AMBER. I have trajectory file for 1000ps with time step 4fs. I considered elapsed time 20ps and averaging the correlation function over different time origin. The result shows an unusual feature. As I am averaging over 200ps it decreases and become negative within 20ps. However, the nature of the plot is changed as I am averaging over 1000ps. The rate of decrease of correlation function gradually decrease as the time upto which time average performed is increased from 200ps to 300ps ...1000ps.
If you kindly suggest me what could be the possible reason for this, it will be very helpful for me. I use a in-house program to compute the correlation function. Is this can be a possible source of error? Then how to varify it? Please let me know,
With best regards
Sindrila
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Received on Wed Sep 07 2011 - 11:00:04 PDT
