Atoms moving too fast OR constraint failure in RATTLE algorithm

From: Diego Alejandro Vargas (vardiego9_at_gmail.com)
Date: Tue Nov 04 2008 - 12:34:00 CST

Hello NAMD users,

I am trying to run an equilibration simulation on a fascin mutant in a water
box. After having minimized the system for 10,000 steps, I am using the
resulting bincoordinates and binvelocities files to try and run the
equilibration simulation in which I first raise the temperature of the
system gradually to 310K and then let it run for 250,000 steps.

For the configuration file at the bottom I keep getting the following error:
*
TCL: Running for 500 steps
ERROR: Constraint failure in RATTLE algorithm for atom 156!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 1695!
ERROR: Constraint failure in RATTLE algorithm for atom 7246!
ERROR: Constraint failure in RATTLE algorithm for atom 67!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 1229!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 5491!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 4055!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 6362!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 133!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 5690!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 1897!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely.
*
I have been looking at various postings on the discussion board and this
seems to be a common problem. I have attempted:

*rigidBonds is set to none:*

ERROR: Atoms moving too fast; simulation has become unstable.
FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.

*rigidBonds is set to water:
*
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Exiting prematurely.

I have also tried making the time step smaller (1 fs), increasing margin,
and using 2 and 4 for nonbondedfreq and fullelectfrequency (instead of 1 and
2). But by implementing these possible solutions together or separate I keep
getting the error that the velocities are too high.

Can anybody help me?

Thank you,
Diego Alejandro Vargas

______________________________________________________________
#############################################################
## JOB DESCRIPTION ##
#############################################################

# Equilibration of
# Fascin mutant ser39ala in a Water Box

#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################

structure /ser39ala_wb.psf
coordinates /ser39ala_wb.pdb
bincoordinates /ser39ala_wb_mn.coor

binvelocities /ser39ala_wb_mn.vel

extendedSystem /ser39ala_wb_mn.xsc

set temperature 310
set outputname /ser39ala_wb_eq

firsttimestep 0

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

# Input
paraTypeCharmm on
parameters /common/par_all27_prot_lipid.inp

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

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp 0
langevinHydrogen off ;# don't couple langevin bath to hydrogens

# Periodic Boundary Conditions
# extendedSystem used.

wrapAll on

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 50
PMEGridSizeY 50
PMEGridSizeZ 50

# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature

# Output
outputName $outputname

restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 100
outputPressure 100

#############################################################
## EXECUTION SCRIPT ##
#############################################################

# Gradual temperature increase:
run 500
for {set i 0} {$i <= $temperature} {incr i 10} {
langevinTemp $i
run 500
}

run 250000 ;# 500ps

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