[gmx-users] REMD log files

N-J.M. Macaluso njmm2 at cam.ac.uk
Mon May 21 12:20:23 CEST 2007


    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.



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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