From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Dec 01 2009 - 11:25:40 CST
A very small change can also occur because by default NAMD zeroes the
center of mass motion of the system on restart (controlled by the
COMmotion parameter). If you're using sane parameters the effects of
this adjustment should be tiny.
Best,
Peter
Roman Petrenko wrote:
> if you didn't use .vel file in restart, the velocities are reassigned
> randomly to correspond to given temperature. if the velocities are
> different, the kinetic energy must be different.
>
>
> On Tue, Dec 1, 2009 at 4:10 AM, Mert Gür <gurmert_at_gmail.com> wrote:
>
>> Hi everyone,
>> After restarting my simulation I observe that the potential energy is
>> exactly the same whereas the kinetic energy differs slightly(Shown below).
>> Where does this very small discrepancy in kinetic energy comes from? I was
>> considering an roundoff error ....but shouldn't be the same round off error
>> included in the potential energy then?
>> Thanks in advance.
>> Best,
>> Mert
>>
>>
>> The last step in my simulation
>>
>>
>> ETITLE: TS BOND ANGLE DIHED
>> IMPRP ELECT VDW BOUNDARY
>> MISC KINETIC TOTAL TEMP
>> TOTAL2 TOTAL3 TEMPAVG PRESSURE
>> GPRESSURE VOLUME PRESSAVG GPRESSAVG
>>
>> ENERGY: 5260000 5413.9691 3062.2414 29.5792
>> 4.9097 -70309.6491 7182.5188 0.0000 0.0000
>> 14544.1653 -40072.2656 309.9742 -39935.0731
>> -39936.8342 310.4262 -189.8211 -212.8311
>> 153601.2160 11.0813 11.4240
>>
>> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 5260000
>> WRITING COORDINATES TO DCD FILE AT STEP 5260000
>> WRITING COORDINATES TO RESTART FILE AT STEP 5260000
>> FINISHED WRITING RESTART COORDINATES
>> WRITING VELOCITIES TO RESTART FILE AT STEP 5260000
>> FINISHED WRITING RESTART VELOCITIES
>>
>>
>>
>> After restarting my simulation
>>
>> ETITLE: TS BOND ANGLE DIHED
>> IMPRP ELECT VDW BOUNDARY
>> MISC KINETIC TOTAL TEMP
>> TOTAL2 TOTAL3 TEMPAVG PRESSURE
>> GPRESSURE VOLUME PRESSAVG GPRESSAVG
>>
>> ENERGY: 0 5413.9691 3062.2414 29.5792
>> 4.9097 -70309.5199 7182.3953 0.0000 0.0000
>> 14543.9888 -40072.4364 309.9705 -39935.7659
>> -39935.7659 309.9705 -190.6196 -212.3171
>> 153601.4592 -190.6196 -212.3171
>>
>>
>>
>>
>
>
>
>
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