From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Jan 06 2006 - 23:35:23 CST
You may have defined basis vectors in your configuration file
(cellBasisVector1, etc). Try removing them as well as the cellOrigin and
wrapAll lines if you have them. These are the options that define a
periodic cell. You will also have to turn off PME since this only applies
to periodic simulation (remove all lines for PME or add "PME no").
I think that will do the trick.
-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of bo baker
Sent: Friday, January 06, 2006 10:13 PM
To: Pedro Borkowski
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: Simulation in vaccum
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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