Sorry, I misread the original post.
-Dan
On Feb 25, 2012, at 9:26 AM, case <case.biomaps.rutgers.edu> wrote:
> On Sat, Feb 25, 2012, Dilraj LAMA wrote:
>
>> 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
>>
>> OLD SIMULATION:
>>
>> NSTEP = 16000500 TIME(PS) = 32531.000 TEMP(K) = 302.19 PRESS = -128.7
>> Etot = -94254.9707 EKtot = 23294.4062 EPtot = -117549.3769
>>
>> 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.
>>
>
> I think Dan's reply is wrong in this case. The more likely culprit is that
> saving to a restart file, then restarting loses some precision. When running
> MD, small differences in starting coordinates (or velocities) quickly produces
> divergent trajectories. This is discussed in the "testing" section of the
> Users' Manual.
>
> To see what happens with a restart, run a short simulation (say 500 steps)
> with ntpr=1, then break it into two parts, again with ntpr=1. You should
> see initial agreement, but by 500 steps, things generally will have
> diverged.
>
> ....hope this helps....dac
>
>
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Received on Sun Feb 26 2012 - 06:00:04 PST
