From: Mert Gür (gurmert_at_gmail.com)
Date: Tue Dec 01 2009 - 11:35:08 CST
Dear Roman,
I am using restart files.That is why I indicated all the lines starting with
"writing" but I should have been clearer .
I asked my question in the first place assuming that I am doing everything
right .
Peter explanation seems to be an answer to my problem.
Thanks you both.
Mert
On Tue, Dec 1, 2009 at 7:25 PM, Peter Freddolino <petefred_at_ks.uiuc.edu>wrote:
> 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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