bugs in NAMD_TI script?

From: shunzhou Wan (uccaswa_at_live.ucl.ac.uk)
Date: Wed Jul 31 2013 - 11:57:28 CDT


I am trying to use namd_ti.pl to analyze the output files from TI
simulation. When I use the command line options, some results are not
what I expected. I am not sure if this is a bug in the script. I did
simulations for a few lambda windows with the same length. When I tried

-f, it shows the first lambda window (lambda=0 in my case) has one data
less than others;
-f -t=60, it seems that only the last window uses 60% of its data, the
others still keep all data;
-f -b=10 -t=60, confirms the "-f -t=60" results as the DDG output is
very close to that from first 60% of all data (the last window uses last
60% data but doesn't contribute much to the final result).

Any suggestions? Thanks in advance!


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