Re: Help with "ERROR: Constraint failure in RATTLE algorithm for atom XXXX!"

From: Corey Fugate (coreyfugate_at_gmail.com)
Date: Mon May 20 2013 - 17:28:21 CDT

Aron, thanks for the suggestions. I have little idea how to implement the
suggestions you've made. I hate to do this, but my config file is below.
Can you show me where to make changes?

Thanks!!!!
#############################################################
## JOB DESCRIPTION ##
#############################################################

# Minimization and Equilibration of
# LAM-protein only

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

structure lamA.psf
coordinates lamA.pdb

set temperature 310
set outputname lamA_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 on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens

# Periodic Boundary Conditions
#cellBasisVector1 50.0 0. 0.0
#cellBasisVector2 0.0 50.0 0.0
#cellBasisVector3 0.0 0 50.0
#cellOrigin -27.4 2.7 -17.1

#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 on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.0
langevinPistonDecay 50.0
langevinPistonTemp $temperature

# Output
outputName $outputname

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

#############################################################
## EXTRA PARAMETERS ##
#############################################################

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

# Minimization
minimize 100
reinitvels $temperature

run 2500 ;# 1ps

On Mon, May 20, 2013 at 1:07 PM, Aron Broom <broomsday_at_gmail.com> wrote:

> tragic.
>
> and you say that atom doesn't appear weird when visualizing? Are you
> recording the DCD every timestep so you can catch the frame just before the
> failure?
>
> Maybe try being extreme in your energy minimization beforehand, as in
> 10,000 steps or something.
>
> Also, are you gradually heating? I usually just initialize to 300K, but
> if you are having problems, maybe do a slow heating of 1K per 1000 steps or
> something. Are you using a Langevin thermostat?
>
>
> On Mon, May 20, 2013 at 12:57 PM, Corey Fugate <coreyfugate_at_gmail.com>wrote:
>
>> Good point. I commented out the lines in the configuration concerning
>> periodic boundary conditions and PME. The run fails with the same error
>> messages, but caused by different atoms.
>>
>>
>> On Mon, May 20, 2013 at 10:16 AM, Aron Broom <broomsday_at_gmail.com> wrote:
>>
>>> you should not have a box if you are doing vacuum simulations.
>>>
>>> you need to not use periodic conditions and not use PME.
>>>
>>> ideally pairdist and cutoff would be essentially infinite.
>>>
>>> not sure if it is the problem, but when you use periodic conditions in a
>>> vacuum, you have two issues:
>>>
>>> 1) PME doesn't work, because you don't have uniform density
>>> 2) if your system has a net charge, you are simulating an infinite
>>> lattice of similarly charged systems which is madness
>>>
>>> ~Aron
>>>
>>>
>>>
>>>
>>> On Mon, May 20, 2013 at 12:08 PM, Corey Fugate <coreyfugate_at_gmail.com>wrote:
>>>
>>>> I am trying to minimize and equilibrate a protein monomer that consists
>>>> of 6525 atoms (protein only). I am doing this is vacuum. I receive the
>>>> following error in my log file -
>>>>
>>>> REINITIALIZING VELOCITIES AT STEP 100 TO 310 KELVIN
>>>> TCL: Running for 2500 steps
>>>> ERROR: Constraint failure in RATTLE algorithm for atom 1917!
>>>> ERROR: Constraint failure; simulation has become unstable.
>>>> ERROR: Exiting prematurely; see error messages above.
>>>>
>>>> This seems to be a common question on the mailing list, so I first read
>>>> through some suggestions described previously. I've tried increasing the
>>>> cutoff and the pairlistdist. This didn't seem to help. It did change the
>>>> atom that seemed to cause the problem, it always seems to be to near the
>>>> surface f the protein. I looked at the pdb in VMD and I don't see any
>>>> unfavorable overlap between this atom and another. Jim Phillips mentioned
>>>> that a good rule of thumb is 1 atom per 10 cubic angstroms. I am working
>>>> with a box with periodic boundary conditions. If I have 6525 atoms, I
>>>> would need a box that had a volume of 65,250 A^3. The original dimensions
>>>> of my box set by the cellBasisVectors are 47,42,44. This would give me a
>>>> box with an area of 80,856 A^3. I went ahead and make the box larger by
>>>> making all the dimensions 50.
>>>>
>>>> Am I missing something obvious? Any suggestions would be great.
>>>>
>>>
>>>
>>>
>>> --
>>> Aron Broom M.Sc
>>> PhD Student
>>> Department of Chemistry
>>> University of Waterloo
>>>
>>
>>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>

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