**From:** Diego Alejandro Vargas (*vardiego9_at_gmail.com*)

**Date:** Tue Nov 04 2008 - 12:34:00 CST

**Next message:**Joshua Adelman: "Re: Atoms moving too fast OR constraint failure in RATTLE algorithm"**Previous message:**Jerome Henin: "Re: How can I specify an exact initial velocity?"**Next in thread:**Joshua Adelman: "Re: Atoms moving too fast OR constraint failure in RATTLE algorithm"**Reply:**Joshua Adelman: "Re: Atoms moving too fast OR constraint failure in RATTLE algorithm"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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

**Next message:**Joshua Adelman: "Re: Atoms moving too fast OR constraint failure in RATTLE algorithm"**Previous message:**Jerome Henin: "Re: How can I specify an exact initial velocity?"**Next in thread:**Joshua Adelman: "Re: Atoms moving too fast OR constraint failure in RATTLE algorithm"**Reply:**Joshua Adelman: "Re: Atoms moving too fast OR constraint failure in RATTLE algorithm"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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