Re: membrane simulation ERROR rattle algorithm

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Tue Jul 05 2011 - 12:54:40 CDT

Hi,

just check which atoms these are. Open the psf+pdb in VMD and create a
selection with "index x y" in the vdw representations. instead of x and y
put the numbers from your error decreased by one.
VMD starts counting atoms at zero and NAMD at one I believe.

So to better explain:
If you get such a message

ERROR: Constraint failure in RATTLE algorithm for atom 44585!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 44884!
ERROR: Constraint failure; simulation has become unstable.

Creating a representation with the selection text "index 44584 44883" will
show you which atoms are problematic.

 I am using the xst, xsc file from the total
> minimization so the dimensions of the system are assigned using this?

I'm not sure. just open the xcs file and see what it contains.

Regards,
Ajasja
On Tue, Jul 5, 2011 at 19:41, Jorgen Simonsen <jorgen589_at_gmail.com> wrote:

> Hi
>
> Thanks for the comments.
>
> So the whole system is minimized for 20.000 steps then I freeze the
> coordinates of the head groups of the lipids(POPC) and a protein
> embedded into the membrane - then I minimize for another 20.000 steps
> - as temperature is assigned to the system it crashes with the before
> mentioned error - I am using the xst, xsc file from the total
> minimization so the dimensions of the system are assigned using this?
>
> I am not sure could it be atoms within a cave or something like this?
>
> On Tue, Jul 5, 2011 at 7:01 PM, Ajasja Ljubetič
> <ajasja.ljubetic_at_gmail.com> wrote:
> > Also, you can try reducing the timestep when you run the simulations. And
> > you'll probably get better results if heat the system slowly. In extreme
> > cases you can try running the simulation for a few steps while heating
> then
> > minimizing then ruining again...
> > The source of the instability is most probably overlap between two atoms,
> > resulting in high vdw energies. So you have to get rid of the overlap.
> > Oh, I just remembered, is your periodic cell of the correct dimensions?
> >
> > Best regards,
> > Ajasja
> >
> >>
> >> Hi all
> >>
> >> I am trying to run a md simulation of a membrane protein imbedded in a
> >> membrane - I have followed the tutorial on membrane proteins but when
> >> I try to apply for an example a equilibration run with the lipid tail
> >> freezing water, protein, and head group I get the following error
> >>
> >>
> >> ERROR: Constraint failure in RATTLE algorithm for atom 44585!
> >> ERROR: Constraint failure; simulation has become unstable.
> >> ERROR: Constraint failure in RATTLE algorithm for atom 44884!
> >> ERROR: Constraint failure; simulation has become unstable.
> >>
> >> I have minimized the whole system with a gradient of
> >>
> >> LINE MINIMIZER REDUCING GRADIENT FROM 39.3483 TO 0.0393483
> >>
> >> but as soon as velocities are assigned to the system(the protein and
> >> water is still frozen setting the b-factor to 1) I get the following
> >> error as stated above. My step size is 2 fs using SHAKE and I am using
> >> the following for electrostatics
> >>
> >> #PME (for full-system periodic electrostatics)
> >> PME yes
> >> # let NAMD determine grid
> >> PMEGridSpacing 1.0
> >>
> >> and the following extra parameters for the pressure
> >>
> >> # Constant Pressure Control (variable volume)
> >> useGroupPressure yes ;# needed for rigid bonds
> >> useFlexibleCell yes ;# no for water box, yes for membrane
> >> useConstantArea no ;#
> >>
> >> I have tried to change the useConstantArea but same problem.
> >>
> >> How to resolve the problem thanks in advance
> >>
> >
> >
>

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