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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