PMF calculation crashes with constraint failure

From: Magnus Andersson (
Date: Sat Jan 25 2014 - 11:02:11 CST


I have equilibrated my system (membrane protein) and have performed a steered MD (moving ligand through channel).

But, the simulations of each of the windows along the reaction coordinate crash immediately:

ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 11603!

The atom is a hydrogen atom on a lipid. This lipid is at the edge of the box. I have checked this visually - I see nothing strange in this region (i.e. no clashes or strained geometries). When I increase the box size, it still crashes but with different atoms.

I'm minimizing for 10,000 steps before starting the PMF simulation. I have also tried equilibrating for 2 more ns (i.e. without colvars), but get crash as soon as I turn colvars on.

Decreasing the time step does not help either. Or margin. Or changing the reference atoms in the colvars file.

Does anyone have an idea of what might be going on?

Some features from the input file:

stepspercycle 20
rigidBonds all
fullElectFrequency 4
nonbondedFreq 2

exclude scaled1-4
1-4scaling 1.0
switching on
vdwForceSwitching yes
switchdist 10.0
cutoff 12.0
pairlistdist 13.5

colvars on

langevin on
langevinDamping 5
langevinTemp 310

useGroupPressure yes
useFlexibleCell yes
LangevinPiston on
LangevinPistonTarget 1.0
LangevinPistonPeriod 200
LangevinPistonDecay 100
LangevinPistonTemp 310

The colvars file:

colvarsTrajFrequency 1000
colvarsRestartFrequency 1000

colvar {
        name Translocation
        width 0.1
        lowerboundary 37
        upperboundary 38
        lowerwallconstant 100.0
        upperwallconstant 100.0
distanceZ {
        main {
                atomnumbers { 59035 }
        ref {
                atomnumbers { (here I use all CA in the transmembrane section of the protein }
           axis ( 0.0, 0.0, 1.0 )
abf {
        colvars Translocation
        fullSamples 1000



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