From: Massimiliano Porrini (mozz76_at_gmail.com)
Date: Sun Mar 30 2014 - 06:49:34 CDT
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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