remlog

Calculate various statistics from a replica log data set.

remlog {<remlog dataset> | <remlog filename>} [out <filename>] [crdidx | repidx][stats [statsout <file>] [printtrips] [reptime <file>]] [lifetime <file>]
[reptimeslope <n> reptimeslopeout <file>] [acceptout <file>] [name <setname>]

<remlog dataset> Previously read-in REM log data.
<remlog filename> REM log file name to read in.
[out <filename>] Write replica/coordinate index versus time to <filename>.
crdidx Print coordinate index vs exchange; output sets contain replica indices.
repidx Print replica index vs exchange; output sets contain coordinate indices.
stats [statsout <file>] Calculate round-trip statistics and optionally write to <file>.
printtrips Print details of each individual round trip.
[reptime <file>] Write time spent at each replica to <file>.
[lifetime <file>] Print lifetime data at each replica to <file>.
[reptimeslope <n>] Calculate the slope of time spent at each replica every <n> exchanges.
[reptimeslopeout <file>] File to write reptimeslope output to.
[acceptout <file>] Write overall exchange acceptances to <file>.
[name <setname>] Output data set name.

Analyze previously read in (via readdata) M-REMD/T-REMD/H-REMD replica log data. Statistics calculated include round-trip time, which is the time needed for a coordinate set to travel from the lowest replica to the highest and back, and the number of exchanges each coordinate spent at each replica. For example, to read in REM log data from an Amber M-REMD run and analyze it:

readdata rem.log.1.save rem.log.2.save dimfile remd.dim as remlog nosearch
remlog rem.log.1.save stats reptime mremdreptime.dat

For an example of remlog analysis applied to actual REMD data, see Roe et al.