[gmx-users] REMD log files

[David van der Spoel]

N-J.M. Macaluso wrote:
> 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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the demux.pl script extracts the temperature profile from the log file. 
it is in src/contrib/scripts
you may need to get the CVS version.
it does not work on energies.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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