Re: membrane simulation ERROR rattle algorithm

From: Jorgen Simonsen (
Date: Tue Jul 05 2011 - 12:41:49 CDT


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
<> 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
>> 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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