From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jul 05 2011 - 13:05:18 CDT
On Tue, Jul 5, 2011 at 1:54 PM, Ajasja Ljubetič
<ajasja.ljubetic_at_gmail.com> wrote:
> 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.
BTW: a tip for lazy people:
use "serial" instead of "index" in the selection string
and you don't need to decrease by one. ;)
axel.
>
>> 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
>> >>
>> >
>> >
>
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
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