AW: Constraint failure in RATTLE

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Apr 01 2014 - 00:11:28 CDT

Did you check the main memory, too?

 

Norman Geist.

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Massimiliano Porrini
Gesendet: Montag, 31. Mrz 2014 18:49
An: Norman Geist
Cc: Namd Mailing List
Betreff: Re: namd-l: Constraint failure in RATTLE

 

On 31 March 2014 07:43, 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.

 

 

Good point and actually I had already considered this explanation, but then
I gave a try
with pmemd.cuda.MPI of Amber12 and it worked very smoothly for "rather long"
runs:
25,000,000 steps with no interruption (time-step = 2 fs).

 

By the way, given that CUDA-enabled versions of NAMD and AMBER work
differently

one from another, I am not that technologically expert to claim that my GPUs
are not broken...
Nevertheless, one code gives problems while the other one does not.

Thanks,
Max

 

 

 

 

Norman Geist.

 

 

Cheers,

Massimiliano

 

 

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Massimiliano Porrini
Gesendet: Sonntag, 30. Mrz 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 Europen 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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