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

From: Aron Broom (broomsday_at_gmail.com)
Date: Mon May 20 2013 - 21:38:01 CDT

so one key thing I note here is that you still have the langevinPiston on
and other things listed under "# Constant Pressure Control (variable
volume)". Since you are in a vacuum, this makes no sense, particularly the
attempt to set the pressure to 1 atm.

I would comment out all of that.

Also, the NAMD manual does a good job of describing all the parameters.

On Mon, May 20, 2013 at 6:28 PM, Corey Fugate <coreyfugate_at_gmail.com> wrote:

> 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
>>
>
>

-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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