From: Jun Zhang (coolrainbow_at_yahoo.cn)
Date: Sat Nov 06 2010 - 23:24:02 CDT
Thank you for your reply. I have tried several ways and I found that for pure liquid water it should be the average over all pairs of HBs along the entire trajectory that can reproduce the Chandler's result.
At first I had computed this only over the trajectory for a particular HB pair and I found that it had a too high fluctuation. Over all pairs in a particular ensemble exhibits a somewhat bias result. These computations were accomplished in VMD by TCL. For average over all pairs of HBs along the entire trajectory, TCL is too slow and I have written a fortran code to perform it and after 13h on an 8-core machine this morning I got the result. It seems that this result can reproduce Chandler's result. I can post the code and data if you need.
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