Strange (very large) atom motions

From: Craig Jolley (
Date: Thu Feb 03 2011 - 17:14:42 CST

Hi everyone...

I'm trying to use NAMD to simulate metal-organic coordination compounds; and
I've set up some simple test simulations using ferroin. I got forcefield
parameters for ferroin by matching normal modes in CHARMM to normal modes
obtained from DFT and modifying the parameter file using Metropolis MC to
improve the mode overlap and frequency agreement; the resulting parameters
might be a little over-refined at this stage but I think they're pretty much

The problem is that when I run an in vacuo simulation of a single ferroin
molecule with no solvent (67 atoms), the simulation crashes with the famous
RATTLE constraint failure error. I know a lot of people have posted to
NAMD-l about this error, but in most cases it seems to be related to
equilibration of a solvated system with periodic boundary conditions; this
is just 67 atoms all alone in space. Sometimes they'll run just fine for
hundreds of ps, then crash with this error. Once I got a bad global
exclusion count error instead. If I set my parameter file to output a DCD
frame at every step, I can watch what goes wrong near the end -- as a rule,
the central Fe atom takes a huge jump in one direction, seemingly without
provocation, and two of the N atoms bonded to it take huge jumps in the
opposite direction. They continue this excursion for a few steps, then
everything starts gyrating around wildly and the simulation crashes. If I
output energies at each frame, I don't see any unusual changes in energy
terms preceding this weird excursion -- it seems completely unprovoked.

The problem comes up a lot with 2 fs timesteps at 300K; if I shorten the
timestep to 1 fs then I still get RATTLE failures, but they take longer to
show up. If I use the langevinFile and langevinCol parameters to remove
Langevin coupling from Fe, the failure looks pretty much the same. If I
turn off Langevin dynamics entirely, then I still get a RATTLE failure but
it doesn't seem to be a result of the same kind of big Fe motion; the motion
just looks really weird from the outset, with very distorted geometries.

The small ferroin simulations were run on my desktop (NAMD 2.6 under Linux)
and encountered the RATTLE error in a larger coordination polymer simulation
on TACC Ranger. Of course I don't know for a fact that the error I
encountered in the big simulation was the same as the small one, but that
seems like a reasonable assumption for now, since the small simulations fail
every time if I wait long enough.

Any ideas about what might be happening here? I've run out of ideas for
things to try; I'm not eager to re-parameterize my forcefield but that's the
only thing I can think of that might still be the problem. My NAMD
configuration file is pasted below; I can send my coordinate/PSF/parameter
files upon request.



structure 3phen-new.psf
coordinates 3phen-min.pdb

set temperature 300
set outputname 3phen_out

firsttimestep 0

# Input
paraTypeCharmm on
parameters /home/craig/Projects/coord_poly/coord_poly.par
#parameters 3phen.par
temperature $temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5

# Integrator Parameters
timestep 2.0
rigidBonds all
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20
pairlistsPerCycle 2

# Constant Temperature Control
langevin on
langevinDamping 5
langevinTemp $temperature
langevinHydrogen off

# Output
outputName $outputname

restartfreq 500000
dcdfreq 1
#dcdfreq 500000
xstFreq 500000
outputEnergies 1
outputPressure 10000

run 5000000

Craig Jolley
Postdoctoral Research Associate
Astrobiology Biogeocatalysis Research Center
Montana State University

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