From: bo baker (bo.bybaker_at_gmail.com)
Date: Fri Jan 06 2006 - 22:12:40 CST
But I run the simulation in vacuum, no water added. Where the
'Periodic cell' comes from? There is only protein there.
> > FATAL ERROR: Periodic cell has become too small for original patch grid!
> > Possible solutions are to restart from a recent checkpoint,
> > increase margin, or disable useFlexibleCell for liquid simulation.
I am very confused.
Thanks for any advice.
Bo
On 1/6/06, Pedro Borkowski <pedro.borkowski_at_gmail.com> wrote:
> hi,
>
> This was previously discussed
>
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/2739.html
>
> hope this helps
>
> -Pedro
>
> On 1/6/06, bo baker <bo.bybaker_at_gmail.com> wrote:
> > Hello, NAMD:
> >
> > I built two models of a transmembrane protein based on two different
> > templates. I would like to do some initial structure refinments:
> > subject the two models to minimization and short simulation in vacuum.
> > This would allow me to compare the two models in energy level as well
> > as geometry level. After this, the model will be inserted into
> > membrane and water for
> > futher MD simulation.
> >
> > I am not sure if NAMD is good for this purpose, simulation protein
> > structure in vacuum. I couldn't find the tutorial or examples. I have
> > tried some steps, but the run was stopped prematured.
> >
> > Here is how I did:
> >
> > --- minimization for 2000 steps
> > --- equil at 310 K for 25000 steps
> >
> > Here are the error messages:
> > For model 1:
> >
> > WRITING COORDINATES TO DCD FILE AT STEP 24000
> > TIMING: 24100 CPU: 2850.66, 0.1199/step Wall: 3000.94,
> > 0.163925/step, 0.132051 hours remaining, 0 kB of memory in use.
> > ENERGY: 24100 543.6413 1486.1952 923.4096 =20
> > 80.5016 -2664.1032 -311.3172 0.0000 =20
> > 0.0000 1922.0600 1980.3873 315.5194 =20
> > 2010.7229 2002.7730 311.0336
> >
> > FATAL ERROR: Periodic cell has become too small for original patch grid!
> > Possible solutions are to restart from a recent checkpoint,
> > increase margin, or disable useFlexibleCell for liquid simulation.
> >
> >
> > For model 2:
> >
> > TIMING: 3200 CPU: 533.74, 0.1147/step Wall: 571.251, 0.121714/step,
> > 0.804667 hours remaining, 0 kB of memory in use.
> > ENERGY: 3200 566.7572 1603.5447 1048.2289 =20
> > 107.6930 -2211.1402 -255.1635 0.0000 =20
> > 0.0000 2051.3032 2911.2233 312.3809 =20
> > 2941.2697 2943.5047 311.9550
> >
> > FATAL ERROR: Periodic cell has become too small for original patch grid!
> > Possible solutions are to restart from a recent checkpoint,
> > increase margin, or disable useFlexibleCell for liquid simulation.
> >
> > I compare the TOTAL and rmsd of the two run. TOTAL are arond 1980
> > (model 1) and 2840 (model 2), rmsd are around 2.31 (model 1) and
> > 2.341 (model 2). When I exam the trajectories, both structures move
> > around entirely but no big change in conformation.
> >
> > Thank you for advice!
> >
> > Regards
> >
> > Bo
> >
> >
>
>
> --
> -Pedro Borkowski
>
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