On Wed, Jun 01, 2011, Lorenzo Gontrani wrote:
> ASCII
>
> NSTEP = 800000 TIME(PS) = 123410.000 TEMP(K) = 500.05 PRESS =
> 0.0
> Etot = 8096.9458 EKtot = 5121.5291 EPtot =
> 2975.4167
> BOND = 1914.0149 ANGLE = 2358.0329 DIHED =
> 681.4969
> 1-4 NB = 167.8290 1-4 EEL = 706.2125 VDWAALS =
> -2310.5917
> EELEC = -541.5777 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> Ewald error estimate: 0.1526E-02
>
> BINARY
>
>
> NSTEP = 800000 TIME(PS) = 123410.000 TEMP(K) = 500.07 PRESS =
> 0.0
> Etot = 8094.2782 EKtot = 5121.6841 EPtot =
> 2972.5941
> BOND = 1914.4745 ANGLE = 2356.1170 DIHED =
> 682.1608
> 1-4 NB = 167.6396 1-4 EEL = 707.7357 VDWAALS =
> -2310.7221
> EELEC = -544.8114 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> Ewald error estimate: 0.1476E-02
>
Please see section 1.3.4 of the Amber11 manual about roundoff errors in MD.
Since pmemd does dynamic load balancing, the division of tasks among
processors may change from one run to the next. This affects the order of
arithmetic manipulations, and hence to differences among trajectories that
otherwise would be the same.
You can run a test with a single thread, and should see the discrepancies go
away.
....dac
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Received on Wed Jun 01 2011 - 05:00:03 PDT
