REMD restart tcl script meaning?

From: Jacob Usadi (jusadi_at_uchicago.edu)
Date: Tue Jul 24 2018 - 12:51:06 CDT

Hello all,

I have been working with the NAMD implementation of REMD, and I now need to
interpret the contents of the tcl scripts generated. The question I'd like
to answer is: what is the meaning of each section of these files?

- Why don't temperature, POTENTIAL, and TEMP seem to match up to the
current replica at the current run number?
- What is dcdindex?
- What is history_file?
- In general, is there documentation somewhere on the run_replica command?
I have not found it yet if it exists.

Example of file contents:

run_replica {i_run 13000 i_step 6500000 index 6 dcdindex 39 index_a 7
index_b 5 temperature 321.17 exchanges_attempted 6500 exchanges_accepted
864 POTENTIAL -67032.03707542503 TEMP 320.8049119929918 history_file {39
file145} checkpointname {} checkpointloc 22} 1.0

Here are my interpretations of each of the parameters given to run_replica:

i_run: The value of the current run.
i_step: The value of the current step.
index: We are in physical replica 6, and that is the index
*dcdindex*: ???
index_a: I believe this is the replica 'below' the current replica against
which comparison is made
index_b: similar, but for the replica above
*temperature*: This appears to be the target temperature for the current
replica. However, I am confused because it does not match the corresponding
value in the history file.
exchanges_attempted: As it says
exchanges_accepted: as it says
*POTENTIAL*: I would assume this is the current potential. However, I do
not find this value at all in history file #6
*TEMP*: similar to potential, it doesn't seem to match up
*history_file*: I do not see how this works

Thanks,
Jacob

-- 
Jacob Usadi
University of Chicago '19
Mathematics / Computational and Applied Mathematics BS

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