AW: ERROR: Constraint failure in RATTLE algorithm for atom 593!

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Feb 04 2013 - 09:33:08 CST

Hi Nutan,

 

there are several possibilities what could cause the problem. The 1st and
most likely is a bad initial structure. This means, that the minimize
possibly was not able to remove all tensions from the system within the
specified minimization steps. To check this, you could use VMD and its NAMD
Plot plugin to plot the total energy from the outputfile of the minimization
and see, if the energy converges or keeps decreasing. As it is not possible
to zoom the plot within vmd directly, you should export the plot and load it
to xmgrace for example (as the energy drops heavily in the 1st steps you are
not able to see clearly if the energy is really constant till the end
because of the range of values on the y axis). If the energy wasn't constant
at the end of the minimization, try increasing the number of minimization
steps further. Also check the outfile for messages like "giving up on x bad
contact" what would indicate superimposed atoms.

 

If all this is not the case, try reducing the timestep to 1. Possibly the 2
fs timestep together with fullelectfreqency 2 (which causes an kinetic
energy drift usually) and no temperature control results in too fast moving
hydrogens which breaks the rigidbonds algorithm, especially at 310 K.

 

Additionally, I don't know if the cell origin should be bigger than the box
itself, see Y dimension and origin.

 

 

Let me know.

 

Norman Geist.

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Nutan Preety
Gesendet: Montag, 4. Februar 2013 13:27
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: ERROR: Constraint failure in RATTLE algorithm for atom 593!

 

 

Hello all namd users,

I am new to namd and trying to run minimization. I increased minimization
steps to 500 to 10,000 but everytime I am getting same type of error. please
help me.

 

 

REINITIALIZING VELOCITIES AT STEP 10000 TO 310 KELVIN.

TCL: Running for 2500 steps

ERROR: Constraint failure in RATTLE algorithm for atom 593!

ERROR: Constraint failure; simulation has become unstable.

ERROR: Constraint failure in RATTLE algorithm for atom 2049!

ERROR: Constraint failure; simulation has become unstable.

ERROR: Constraint failure in RATTLE algorithm for atom 570!

ERROR: Constraint failure; simulation has become unstable.

ERROR: Constraint failure in RATTLE algorithm for atom 1167!

ERROR: Constraint failure; simulation has become unstable.

ERROR: Constraint failure in RATTLE algorithm for atom 73!

ERROR: Constraint failure; simulation has become unstable.

ERROR: Constraint failure in RATTLE algorithm for atom 10!

ERROR: Constraint failure; simulation has become unstable.

ERROR: Constraint failure in RATTLE algorithm for atom 170!

ERROR: Constraint failure; simulation has become unstable.

ERROR: Constraint failure in RATTLE algorithm for atom 185!

ERROR: Constraint failure; simulation has become unstable.

ERROR: Exiting prematurely; see error messages above.

 

 

 

 

Below is the configuration file content:

 

# Minimization and Equilibration of

# Ubiquitin in a Water Box

 

 

#############################################################

## ADJUSTABLE PARAMETERS ##

#############################################################

 

structure JBP_wb.psf

coordinates JBP_wb.pdb

 

set temperature 310

set outputname JBP_wb_eq

 

firsttimestep 0

 

 

#############################################################

## SIMULATION PARAMETERS ##

#############################################################

 

# Input

paraTypeCharmm on

parameters par_all27_prot_lipid.inp

temperature $temperature

 

 

# Force-Field Parameters

exclude scaled1-4

1-4scaling 1.0

cutoff 12.0

switching on

switchdist 10.0

pairlistdist 14.0

 

 

# Integrator Parameters

timestep 2.0 ;# 2fs/step

rigidBonds all ;# needed for 2fs steps

nonbondedFreq 1

fullElectFrequency 2

stepspercycle 10

 

 

# Constant Temperature Control

langevin off ;# do langevin dynamics

langevinDamping 5 ;# damping coefficient (gamma) of 1/ps

langevinTemp $temperature

langevinHydrogen off ;# don't couple langevin bath to hydrogens

 

 

# Periodic Boundary Conditions

cellBasisVector1 42.0 0. 0.0

cellBasisVector2 0.0 44.0 0.0

cellBasisVector3 0.0 0 47.0

cellOrigin -18.077 45.61 27.75

 

wrapAll on

 

 

# PME (for full-system periodic electrostatics)

PME yes

PMEGridSpacing 1.0

 

#manual grid definition

#PMEGridSizeX 45

#PMEGridSizeY 45

#PMEGridSizeZ 48

 

 

# Constant Pressure Control (variable volume)

useGroupPressure yes ;# needed for rigidBonds

useFlexibleCell no

useConstantArea no

 

langevinPiston OFF

langevinPistonTarget 1.01325 ;# in bar -> 1 atm

langevinPistonPeriod 100.0

langevinPistonDecay 50.0

langevinPistonTemp $temperature

 

 

# Output

outputName $outputname

 

restartfreq 500 ;# 500steps = every 1ps

dcdfreq 250

xstFreq 250

outputEnergies 100

outputPressure 100

binaryoutput no ;#give me the pdb instead of .coor

 

 

#############################################################

## EXTRA PARAMETERS ##

#############################################################

 

 

#############################################################

## EXECUTION SCRIPT ##

#############################################################

 

# Minimization

minimize 10000

reinitvels $temperature

 

run 2500 ;# 5ps

 

 

-- 
Regards,
 
*****
Nutan Chauhan
Ph.D. Student,
Department of Biotechnology,
BIT, Mesra
Ranchi 835215
Jharkhand
INDIA

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