Re: Atoms moving too fast OR constraint failure in RATTLE algorithm

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Tue Nov 04 2008 - 12:58:44 CST

Hi Diego,

Here's a couple of things to check:
1. It looks like your barostat temperature is set immediately to 310.
I would move the line:
> langevinPistonTemp $temperature
into the loop that gradually increases the temperature, so that your
langevin thermostat and langevin piston barostat agree. I think this
might be the largest problem.
2. What is going on with your box size? Look in the .xst file to see
how it's changing over time.
3. Does your error occur immediately or after a couple of heating
cycles? I'm assuming it crashes immediately.
4. You might want to try increasing the length of equilibration after
each temperature jump and see if that helps things. Check the
progression of the temperature and see if it has settled to the
desired temp before you increase it again.
5. If you system has a poor initial setup, it is possible that you
might need a time step smaller than 1 fs for the initial bit of the
heating. Try 0.5 fs and see if that helps.
6. Are the errors always with the same atoms? Visually inspect those
atoms to see if they are in trouble spots or if they have a high beta
factor associated with them.

Josh

On Nov 4, 2008, at 10:34 AM, Diego Alejandro Vargas wrote:

> 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
>

------------------------------------------------------------------------------------------------------
Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley http://nature.berkeley.edu/~jadelman
Berkeley, CA 94720 USA jadelman_at_berkeley.edu
------------------------------------------------------------------------------------------------------

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