Re: Constraint failure in RATTLE

From: Francesco Pietra (francesco.pietra_at_accademialucchese.it)
Date: Mon Mar 31 2014 - 02:29:48 CDT

>
> memory errors can cause such a behavior. Especially broken GPUs.
>

That is useful suggestion, particularly as the problem proved erratic and
occurred twice after 5,000,000 steps.

The are no GPUs involved. Crash occurred during accelMD. NAMD is not yet
able to run accelMD on GPUs, as you know.

francesco

On Mon, Mar 31, 2014 at 7:43 AM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:

> Just as a additional hint, memory errors can cause such a behavior.
> Especially broken GPUs. So you might have a look on specific nodes being
> present while the error occurs and not being present if the error is absent.
>
>
>
> Norman Geist.
>
>
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Massimiliano Porrini
> *Gesendet:* Sonntag, 30. März 2014 13:50
> *An:* Francesco Pietra
> *Cc:* NAMD
> *Betreff:* Re: namd-l: Constraint failure in RATTLE
>
>
>
> Hi,
>
>
>
> I had been experiencing this problem rather frequently in my 2 types of
> simulation:
>
>
>
>
>
> 1) With namd2.9 - CUDA enabled CVS-2013-07-22_Linux-x86_64-multicore .
>
>
>
> Each time the RATTLE algorithm failed for a different carbon atom, but
>
> always the same type, CTL2, which is a carbon atom of an aliphatic tail
>
> of a amphiphile molecule.
>
>
>
> I am using CHARMM36 force field parameters.
>
>
>
>
>
> 2) The second has happened within another compound, but with either
>
> an aromatic carbon, CA, or an sp3 aliphatic carbon, CG331, bound to the
> benzene ring.
>
>
>
> In this case, the failure was encountered with both the CUDA enabled and
> lone CPU version
>
> (2.9 and the following CVS: 2013-11-09, 2014-01-13 and 2014-03-23).
>
>
>
> However this compound was parametrised by me with the ffTK of VMD, hence
>
> I have always attributed the failure to an non-optimal modellisation.
>
>
>
> In this case, I have also tried to run the simulation with the following
> "slower" and more accurate
>
> settings (after the system total energy was sufficiently minimised: it has
> plateaued for tens of thousands
>
> of steps..!):
>
>
>
>
>
> timestep 1.0
> rigidBonds all
> nonbondedFreq 1
> fullElectFrequency 1
> stepspercycle 10
>
>
>
>
> But unfortunately no luck!
>
>
>
> Regards,
>
> Massimiliano
>
>
>
>
>
> PS in all the cases I have just restarted the simulation and reached
>
> the desired simulation time (by the way, I want to point out that
>
> for some simulation portions no RATTLE failure occurred).
>
>
>
>
>
>
>
>
>
>
>
> On 30 March 2014 09:31, Francesco Pietra <chiendarret_at_gmail.com> wrote:
>
> Hello:
>
> This is to report a rather unusual "constraint failure in RATTLE algorithm
> for atom 520" during non-periodic accelMD under GB conditions with namd2.9.
>
> Atom 520 is CA of a TRP residue that makes part seven residues at one end
> of a 37-residue peptide, and which are under rmsd colvars, keeping them as
> an alpha-helix stretch.
>
> This accelMD followed a series of similar accelMD, which were started
> after a series of T-REMD under either non-periodic GB or periodic explicit
> conditions. There was no crash before the one above. Otherwise, folding was
> going on smoothly, albeit still far from completion.
>
> Graphics does not suggest any unusual situation for CA 520. Also, namd
> plot with the log file shows constant energy, even when magnified.
>
>
>
> francesco pietra
>
>
>
>
>
> --
> Dr Massimiliano Porrini
> Institut Européen de Chimie et Biologie (IECB)
> CNRS UMR 5248 Chimie et Biologie des Membranes et des Nano-objets (CBMN)
> 2, rue Robert Escarpit
> 33607 Pessac Cedex
> France
> http://www.iecb.u-bordeaux.fr/
>
> Emails: m.porrini_at_iecb.u-bordeaux.fr
> M.porrini_at_ed.ac.uk
> maxp_at_iesl.forth.gr
> mozz76_at_gmail.com
>
>
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