Re: Simulation in vaccum

From: bo baker (bo.bybaker_at_gmail.com)
Date: Sat Jan 07 2006 - 19:12:56 CST

I don't define any basis vectors in my conf file, and no line of PME.
That is why I am very confused. May be the default setting in NAMD
includes the cellBasis Vectors and PME. So I should add lines such as
'PME no' to avoid the periodic simulation? Or simply NAMD does not
support vaccum simulation?

Thanks for advices

Bo

On 1/6/06, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> 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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