Hi,
Thanks for your previous responses to my questions on REMD. I have a
general question about understanding REMD in gromacs. Can someone break
down how to read the .log file? For instance, one of the main goals I have
is to graph the time evolution of temperature exchange for a specific
replica (eg. Replica 4). I would like to show that my simulation was able
to have a random walk in temperature space. Furthermore, how would I show a
random walk in potential energy space? My trouble is that I don't know
where to extract this information from an REMD log file. There is one small
section from my .log file after an REMD run below for an example.
Thanks,
Max
Replica exchange at step 200 time 0.2 Repl 5 <-> 6 dE = 4.948e+00 Repl ex 0
1 2 3 4 5 6 7 8 9 x 10 11 x 12 13 14 15 Repl pr .00 .00 .01 .00 1.0 .71 .01
Step Time Lambda
300 0.30000 0.00000
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.005681 5 6 0.001385
After LINCS 0.000021 54 56 0.000007
Energies (kJ/mol)
Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
2.09992e+02 1.44621e+01 7.48359e+00 9.96865e+01 9.55457e+02
LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR) Coul. recip.
1.02075e+04 -2.66400e+02 -6.36147e+04 1.24965e+01 -8.58854e+03
Potential Kinetic En. Total Energy Temperature Pressure (bar)
-6.09626e+04 1.12505e+04 -4.97121e+04 3.16629e+02 -6.97164e-01
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