Re: NAMD2.9-ERROR: Constraint failure in RATTLE algorithm for atom!

From: Richard (
Date: Fri Aug 25 2017 - 23:03:00 CDT

If you are using explicit solvent it is usually a good idea to fix or restrain the protein/ligand atoms and let the solvent atoms equlibrate after heating the system. Once the solvent is equlibrated you can then run a second phase with the protein unconstrained. I wouldn't attribute this behavior to the software just yet.


On Aug 25, 2017 11:47 PM, 王茜茜 <> wrote:
Dear developer,
   Recently, I need to use NAMD2.9 source code (because I want to learn Plumed2.1.2). After installing both two softwares, I  tested the given examples in the manual and both worked well. 
    Then, I tested my system that worked well previously with NAMD_2.11_Linux-x86_64-multicore-CUDA. However, when using NAMD2.9 source code, it always gave the error:
ERROR: Constraint failure in RATTLE algorithm for atom 107!
ERROR: Constraint failure; simulation has become unstable.
The following is my conf:
amber             yes
parmfile          com_sol.prmtop
ambercoor         com_sol.inpcrd
set temperature   310
set outputname    ../output/md

# Continuing a job from the restart files
if {1} {
set inputname      eq3
binCoordinates     ../output/$inputname.restart.coor       
binVelocities      ../output/$inputname.restart.vel  ;# remove the "temperature" entry if you use this!
extendedSystem   ../output/$inputname.restart.xsc
exclude             scaled1-4
1-4scaling          0.833333
cutoff              12.0
switching           off
switchdist          10.0
pairlistdist        13.5

# Integrator Parameters
timestep            2.0  ;# 2fs/step
rigidBonds          all  ;# needed for 2fs steps
nonbondedFreq       1
fullElectFrequency  2  
stepspercycle       20
rigidTolerance      0.00001

# Constant Temperature Control
langevin            on    ;# do langevin dynamics
langevinDamping     1     ;# damping coefficient (gamma) of 5/ps
langevinTemp        $temperature
langevinHydrogen    off    ;# don't couple langevin bath to hydrogens

# Periodic Boundary Conditions
wrapAll             on

# PME (for full-system periodic electrostatics)
PME                 yes
PMEGridSizeX        72
PMEGridSizeY        72
PMEGridSizeZ        80

# Constant Pressure Control (variable volume)
if {1} {
useGroupPressure      yes ;# needed for 2fs steps
useFlexibleCell       no  ;# no for water box, yes for membrane
useConstantArea       no  ;# no for water box, yes for membrane

langevinPiston        on
langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
langevinPistonPeriod  200.0
langevinPistonDecay   100.0
langevinPistonTemp    $temperature

# Output
outputName          $outputname

restartfreq         1000     ;# 500steps = every 1ps
dcdfreq             1000
xstFreq             1000

run  25000
   I have minimized the system for many times and tried other systems, and obtained same error. Actually, my system worked well in other machines with NAMD2.9 source code. So, I donot know why. It confused me for two weeks. so, dear developer, may you give me a help? 

Macao university

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