From: Guoxiong Su (scorpian.susu_at_gmail.com)
Date: Sun Dec 12 2010 - 14:11:37 CST
Dear NAMD users and developers,
I am a second-year graduate student and am using the NAMD program with the
module of the Replica Exchange Method (REM) for my research.
I am confused by the names of the output files generated by the REM scripts.
For example, the output files were sorted by numbers as the following:
I am not sure about how the output files were organized from the TCl scripts
for the REM simulations. Were the files sorted by the order of initial
temperatures in the simulations or by the order of the replica numbers? It
is particularly confusing when I read about the content of "only the
temperatures were exchanged" in the User Guide. If the output files were
sorted by the order of replica numbers then I assumed that the output files
were consisted of scrambled trajectories from the exchanged temperatures. If
so, is there a script that I could use to extract the dcd file for a
particular temperature that I am interested in (e.g. 300K) from all these 40
dcd out files?
I would appreciate it very much if anyone can help clarify my confusion.
Department of Physics
University of Houston
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