Hi,
I believe this is related to the fact that the energy values printed
in the output file are not precisely synchronized with the coordinates
due to the leapfrog integration scheme. See this thread for some more
detail:
http://structbio.vanderbilt.edu/archives/amber-archive/2007/1333.php
-Dan
On Sat, Feb 25, 2012 at 3:32 AM, Dilraj LAMA <dilrajl.bii.a-star.edu.sg> wrote:
> Dear Amber Users,
> I was running a simulation which got stalled after a
> period due to some reason. I was saving the restart file (.rst) every
> one nanosecond. Hence I restarted the job with the latest restart file
> as input. Then I compared the energy values in the beginning of the
> new run and the value at the same time step in the old simulation.
>
> I was expecting the energy values to be identical. However they are
> not. Below are the values from the two simulation run.
>
> NEW SIMULATION:
>
> NSTEP = 500 TIME(PS) = 32531.000 TEMP(K) = 301.10 PRESS = 39.9
> Etot = -94460.3737 EKtot = 23209.8266 EPtot =
> -117670.2004
> BOND = 596.0055 ANGLE = 1584.8678 DIHED =
> 1982.9901
> 1-4 NB = 675.1219 1-4 EEL = 7437.2640 VDWAALS =
> 14792.4105
> EELEC = -144738.8602 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 10380.1481 VIRIAL = 10052.1785 VOLUME =
> 380816.0028
> Density =
> 1.0110
> Ewald error estimate: 0.1281E-03
>
> ------------------------------------------------------------------------------
>
>
> OLD SIMULATION:
>
> NSTEP = 16000500 TIME(PS) = 32531.000 TEMP(K) = 302.19 PRESS = -128.7
> Etot = -94254.9707 EKtot = 23294.4062 EPtot =
> -117549.3769
> BOND = 602.1720 ANGLE = 1558.0063 DIHED =
> 1989.9839
> 1-4 NB = 688.5245 1-4 EEL = 7435.4022 VDWAALS =
> 14663.2548
> EELEC = -144486.7205 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 10496.6578 VIRIAL = 11554.9064 VOLUME =
> 380809.5500
> Density =
> 1.0110
> Ewald error estimate: 0.7322E-05
>
> ------------------------------------------------------------------------------
>
> I would expect the values to be identical in both cases since I am
> restarting my simulation with the same coordinate and velocity values
> at this particular time step supplied through restart file.
>
> Am I not correct or am I missing some important fundamental concept?
>
> I will be glad if you can give me your opinion.
>
> Thank you,
> Dilraj.
>
>
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Received on Sat Feb 25 2012 - 05:30:02 PST
