From: bo baker (bo.bybaker_at_gmail.com)
Date: Wed Jan 11 2006 - 16:20:37 CST
Hi, Peter:
Thanks you for your suggestion. I set the dcdFreq at 2500, so there
was one one trajectory when the run stopped. I can't tell any thing
unusaual from VMD. May re-run it with reduced decFreq.
I also try to modify the .conf file by adding one line: " rigidbonds
all ", and reduce 'margin' from 15 to 2, and run it with namd2. It
went throngh. No errors and warnings. I have included the .conf files
as attachments. The n62-NPT2-011006.conf is the one caused the errors,
while n62-NPT3-011006.conf had no problem at all.
My question is, when 'rigidbond set to all', is this still MD
simulation, or just equilibrate the system? How can one tell the
difference between equilibration and simulation at constant
temperature and conctant pressure? I look at the NAMD tutorial and the
example of "Building Gramicidin A'. I can't tell the difference. Or
may be in NAMD, equilibration without any constrains does the same job
as simulation? I am very confused.
Thanks for advice
On 1/10/06, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> Dear Bo,
> have you viewed the resulting trajectory in VMD? Do you see anything
> unusual happening, like an atom or group flying off? This still sounds
> like an issue of a system not being minimized enough or something along
> those lines. Also, I'd recommend trying with a timestep of 1 instead of 2.
> Peter
>
> bo baker wrote:
>
> >Hello, NAMD:
> >
> >I am still stucked by the velocity errors. With the suggestions from
> >others, I have modified the '.conf' file: delete the
> >'cellBasisVectors', padding my OME grid sizes a bit more; choose
> >'useflexsibleCell no'. All these efforts allow the simulation to a bit
> >longer, but still stopped premature:
> >
> >TIMING: 23500 CPU: 4960.12, 3.24876/step Wall: 5015.77,
> >3.28091/step, 109.819 hours remaining, 0 kB of memory in use.
> >ENERGY: 23500 16407.7215 10176.8444 1125.4231
> >116.4013 -168531.4559 15352.3312 0.0000
> >0.0000 42943.8007 -82408.9338 321.8909
> >-78444.0002 -78785.3512 308.5296 15004.4553
> >119.9913 436736.3972 -5.5312 -3.9712
> >
> >ERROR: Atom 1766 velocity is -6825.09 -441.432 -309.29 (limit is 5000)
> >ERROR: Atoms moving too fast; simulation has become unstable.
> >ERROR: Exiting prematurely.
> >==========================================
> >WallClock: 5700.964844 CPUTime: 5633.370117 Memory: 0 kB
> >Program finished.
> >
> >
> >I have included my .conf file as an attachment. Thanks for advice.
> >
> >
> >Bo
> >
> >
>
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