[gmx-users] REMD and T autocorrelation

elena.mol at mail.com elena.mol at mail.com
Mon Aug 2 16:41:32 CEST 2010

Dear gmx-ers, I have aquestion regarding replica exchange and temperature autocorrelation..
I want to calculate thetemperature (T) autocorrelation function from a REMD simulation.

Is it ok to “directly”use g_energy on the .edr files of my trajectory in order to obtain an.xvg file with T vs. t, and then g_analyze on this .xvg files toobtain the autocorrelation function? (as one would do on a “standard”MD without replica exchange) 
Or do I need to “demux”the trajectory files with demux.pl to really monitor each replica inits temperature “jumps”? But, in this latter case..... theprocedure described in http://www.gromacs.org/Documentation/How-tos/REMD
post-processingacts on .xtc files (through the use of .log files).  The .edr files remain unchanged. Am I missing something trivial?....... 
What am i monitoring if i do g_energy + g_analyze on "raw" (not demuxed) .edr files from a REMD simulation?......

Many thanks in advance
best regards
Elena Molteni


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