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

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? 

Qianqian

Macao university