you are right, this "rem" test is from an earlier test version and does
not match results from correct code.
use the "Replica Exchange test suite" from the AMBER web site (as Dave
Case pointed out).
Carlos
> I do have a directory
>named rem. In there, there is a Run.rem script which I ran (I edited the
>Makefile to go into that directory and run the script). I used 4
>processors and the simulation ran to completion. However the output files
>look different (although, not unreasonable).
>
>The first few lines of the rem.log I produced looks like this:
>
> # replica exchange log file
> # Replica #, Velocity Scaling Factor, T, Eptot, Temp0, NewTemp0
> # exchange 1
> 1 -1.00 275.68 -547.98 267.00 267.00
> 2 -1.00 298.43 -544.73 283.00 283.00
>
>the rem.log.save file looks like this:
>
> # replica exchange log file
> # Replica Number, Scaling Factor, T, Eptot, Temp0, NewTemp0
> # exchange 1
> 1 -1.00 268.20 -541.88 267.00 267.00
> 2 -1.00 277.70 -529.46 283.00 283.00
>
>Using the coordinates and mdin file for replica 1, I performed the
>simulation up to the point right before exchange using a serial
>version of amber8 (one that passses all the
>sander tests as well). I get
>
> NSTEP = 100 TIME(PS) = 45646.100 TEMP(K) = 275.68 PRESS = 0.0
> Etot = -353.4957 EKtot = 194.4827 EPtot = -547.9784
>
>
> A V E R A G E S O V E R 100 S T E P S
>
>
> NSTEP = 100 TIME(PS) = 45646.100 TEMP(K) = 268.44 PRESS = 0.0
> Etot = -352.5915 EKtot = 189.3727 EPtot = -541.9643
>
>So it looks like the rem.log.save file used the average values for energy
>and temperature. Now, I know that's incorrect, and perhaps that's from
>some earlier version. So it looks like the code is working properly (it's
>certainly picking out the adequate energy and temperature). Although I'm
>left uncertain if the compilation worked properly. Has anyone else come
>across this problem before?? Any simple tests that can be run??
>
>
>Thanks
>
>-Sergio
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Received on Fri Sep 10 2004 - 14:53:00 PDT
